Bio.Align.Applications package

Module contents

Alignment command line tool wrappers (OBSOLETE).

We have decided to remove this module in future, and instead recommend building your command and invoking it via the subprocess module directly.

class Bio.Align.Applications.MuscleCommandline(cmd='muscle', **kwargs)

Bases: AbstractCommandline

Command line wrapper for the multiple alignment program MUSCLE.

http://www.drive5.com/muscle/

Notes

Last checked against version: 3.7, briefly against 3.8

References

Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113.

Examples

>>> from Bio.Align.Applications import MuscleCommandline
>>> muscle_exe = r"C:\Program Files\Alignments\muscle3.8.31_i86win32.exe"
>>> in_file = r"C:\My Documents\unaligned.fasta"
>>> out_file = r"C:\My Documents\aligned.fasta"
>>> muscle_cline = MuscleCommandline(muscle_exe, input=in_file, out=out_file)
>>> print(muscle_cline)
"C:\Program Files\Alignments\muscle3.8.31_i86win32.exe" -in "C:\My Documents\unaligned.fasta" -out "C:\My Documents\aligned.fasta"

You would typically run the command line with muscle_cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='muscle', **kwargs): Initialize the class.

property anchors

Use anchor optimisation in tree dependent refinement iterations

This property controls the addition of the -anchors switch, treat this property as a boolean.

property anchorspacing

Minimum spacing between anchor columns

This controls the addition of the -anchorspacing parameter and its associated value. Set this property to the argument value required.

property brenner

Use Steve Brenner’s root alignment method

This property controls the addition of the -brenner switch, treat this property as a boolean.

property center

Center parameter - should be negative

This controls the addition of the -center parameter and its associated value. Set this property to the argument value required.

property cluster

Perform fast clustering of input sequences, use -tree1 to save tree

This property controls the addition of the -cluster switch, treat this property as a boolean.

property cluster1

Clustering method used in iteration 1

This controls the addition of the -cluster1 parameter and its associated value. Set this property to the argument value required.

property cluster2

Clustering method used in iteration 2

This controls the addition of the -cluster2 parameter and its associated value. Set this property to the argument value required.

property clw

Write output in CLUSTALW format (with a MUSCLE header)

This property controls the addition of the -clw switch, treat this property as a boolean.

property clwout

Write CLUSTALW output (with MUSCLE header) to specified filename

This controls the addition of the -clwout parameter and its associated value. Set this property to the argument value required.

property clwstrict

Write output in CLUSTALW format with version 1.81 header

This property controls the addition of the -clwstrict switch, treat this property as a boolean.

property clwstrictout

Write CLUSTALW output (with version 1.81 header) to specified filename

This controls the addition of the -clwstrictout parameter and its associated value. Set this property to the argument value required.

property core

Do not catch exceptions

This property controls the addition of the -core switch, treat this property as a boolean.

property diagbreak

Maximum distance between two diagonals that allows them to merge into one diagonal

This controls the addition of the -diagbreak parameter and its associated value. Set this property to the argument value required.

property diaglength

Minimum length of diagonal

This controls the addition of the -diaglength parameter and its associated value. Set this property to the argument value required.

property diagmargin

Discard this many positions at ends of diagonal

This controls the addition of the -diagmargin parameter and its associated value. Set this property to the argument value required.

property diags

Find diagonals (faster for similar sequences)

This property controls the addition of the -diags switch, treat this property as a boolean.

property dimer

Use faster (slightly less accurate) dimer approximationfor the SP score

This property controls the addition of the -dimer switch, treat this property as a boolean.

property distance1

Distance measure for iteration 1

This controls the addition of the -distance1 parameter and its associated value. Set this property to the argument value required.

property distance2

Distance measure for iteration 2

This controls the addition of the -distance2 parameter and its associated value. Set this property to the argument value required.

property fasta

Write output in FASTA format

This property controls the addition of the -fasta switch, treat this property as a boolean.

property fastaout

Write FASTA format output to specified filename

This controls the addition of the -fastaout parameter and its associated value. Set this property to the argument value required.

property gapextend

Gap extension penalty

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Gap open score - negative number

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property group

Group similar sequences in output

This property controls the addition of the -group switch, treat this property as a boolean.

property html

Write output in HTML format

This property controls the addition of the -html switch, treat this property as a boolean.

property htmlout

Write HTML output to specified filename

This controls the addition of the -htmlout parameter and its associated value. Set this property to the argument value required.

property hydro

Window size for hydrophobic region

This controls the addition of the -hydro parameter and its associated value. Set this property to the argument value required.

property hydrofactor

Multiplier for gap penalties in hydrophobic regions

This controls the addition of the -hydrofactor parameter and its associated value. Set this property to the argument value required.

property in1

First input filename for profile alignment

This controls the addition of the -in1 parameter and its associated value. Set this property to the argument value required.

property in2

Second input filename for a profile alignment

This controls the addition of the -in2 parameter and its associated value. Set this property to the argument value required.

property input

Input filename

This controls the addition of the -in parameter and its associated value. Set this property to the argument value required.

property le

Use log-expectation profile score (VTML240)

This property controls the addition of the -le switch, treat this property as a boolean.

property log

Log file name

This controls the addition of the -log parameter and its associated value. Set this property to the argument value required.

property loga

Log file name (append to existing file)

This controls the addition of the -loga parameter and its associated value. Set this property to the argument value required.

property matrix

path to NCBI or WU-BLAST format protein substitution matrix - also set -gapopen, -gapextend and -center

This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

property maxdiagbreak

Deprecated in v3.8, use -diagbreak instead.

This controls the addition of the -maxdiagbreak parameter and its associated value. Set this property to the argument value required.

property maxhours

Maximum time to run in hours

This controls the addition of the -maxhours parameter and its associated value. Set this property to the argument value required.

property maxiters

Maximum number of iterations

This controls the addition of the -maxiters parameter and its associated value. Set this property to the argument value required.

property maxtrees

Maximum number of trees to build in iteration 2

This controls the addition of the -maxtrees parameter and its associated value. Set this property to the argument value required.

property minbestcolscore

Minimum score a column must have to be an anchor

This controls the addition of the -minbestcolscore parameter and its associated value. Set this property to the argument value required.

property minsmoothscore

Minimum smoothed score a column must have to be an anchor

This controls the addition of the -minsmoothscore parameter and its associated value. Set this property to the argument value required.

property msf

Write output in MSF format

This property controls the addition of the -msf switch, treat this property as a boolean.

property msfout

Write MSF format output to specified filename

This controls the addition of the -msfout parameter and its associated value. Set this property to the argument value required.

property noanchors

Do not use anchor optimisation in tree dependent refinement iterations

This property controls the addition of the -noanchors switch, treat this property as a boolean.

property nocore

Catch exceptions

This property controls the addition of the -nocore switch, treat this property as a boolean.

property objscore

Objective score used by tree dependent refinement

This controls the addition of the -objscore parameter and its associated value. Set this property to the argument value required.

property out

Output filename

This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

property phyi

Write output in PHYLIP interleaved format

This property controls the addition of the -phyi switch, treat this property as a boolean.

property phyiout

Write PHYLIP interleaved output to specified filename

This controls the addition of the -phyiout parameter and its associated value. Set this property to the argument value required.

property phys

Write output in PHYLIP sequential format

This property controls the addition of the -phys switch, treat this property as a boolean.

property physout

Write PHYLIP sequential format to specified filename

This controls the addition of the -physout parameter and its associated value. Set this property to the argument value required.

property profile

Perform a profile alignment

This property controls the addition of the -profile switch, treat this property as a boolean.

property quiet

Do not display progress messages

This property controls the addition of the -quiet switch, treat this property as a boolean.

property refine

Only do tree dependent refinement

This property controls the addition of the -refine switch, treat this property as a boolean.

property refinew

Only do tree dependent refinement using sliding window approach

This property controls the addition of the -refinew switch, treat this property as a boolean.

property refinewindow

Length of window for -refinew

This controls the addition of the -refinewindow parameter and its associated value. Set this property to the argument value required.

property root1

Method used to root tree in iteration 1

This controls the addition of the -root1 parameter and its associated value. Set this property to the argument value required.

property root2

Method used to root tree in iteration 2

This controls the addition of the -root2 parameter and its associated value. Set this property to the argument value required.

property scorefile

Score file name, contains one line for each column in the alignment with average BLOSUM62 score

This controls the addition of the -scorefile parameter and its associated value. Set this property to the argument value required.

property seqtype

Sequence type

This controls the addition of the -seqtype parameter and its associated value. Set this property to the argument value required.

property smoothscoreceil

Maximum value of column score for smoothing

This controls the addition of the -smoothscoreceil parameter and its associated value. Set this property to the argument value required.

property smoothwindow

Window used for anchor column smoothing

This controls the addition of the -smoothwindow parameter and its associated value. Set this property to the argument value required.

property sp

Use sum-of-pairs protein profile score (PAM200)

This property controls the addition of the -sp switch, treat this property as a boolean.

property spn

Use sum-of-pairs protein nucleotide profile score

This property controls the addition of the -spn switch, treat this property as a boolean.

property spscore

Compute SP objective score of multiple alignment

This controls the addition of the -spscore parameter and its associated value. Set this property to the argument value required.

property stable

Do not group similar sequences in output (not supported in v3.8)

This property controls the addition of the -stable switch, treat this property as a boolean.

property sueff

Constant used in UPGMB clustering

This controls the addition of the -sueff parameter and its associated value. Set this property to the argument value required.

property sv

Use sum-of-pairs profile score (VTML240)

This property controls the addition of the -sv switch, treat this property as a boolean.

property tree1

Save Newick tree from iteration 1

This controls the addition of the -tree1 parameter and its associated value. Set this property to the argument value required.

property tree2

Save Newick tree from iteration 2

This controls the addition of the -tree2 parameter and its associated value. Set this property to the argument value required.

property usetree

Use given Newick tree as guide tree

This controls the addition of the -usetree parameter and its associated value. Set this property to the argument value required.

property verbose

Write parameter settings and progress

This property controls the addition of the -verbose switch, treat this property as a boolean.

property version

Write version string to stdout and exit

This property controls the addition of the -version switch, treat this property as a boolean.

property weight1

Weighting scheme used in iteration 1

This controls the addition of the -weight1 parameter and its associated value. Set this property to the argument value required.

property weight2

Weighting scheme used in iteration 2

This controls the addition of the -weight2 parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.ClustalwCommandline(cmd='clustalw', **kwargs)

Bases: AbstractCommandline

Command line wrapper for clustalw (version one or two).

http://www.clustal.org/

Notes

Last checked against versions: 1.83 and 2.1

References

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.

Examples

>>> from Bio.Align.Applications import ClustalwCommandline
>>> in_file = "unaligned.fasta"
>>> clustalw_cline = ClustalwCommandline("clustalw2", infile=in_file)
>>> print(clustalw_cline)
clustalw2 -infile=unaligned.fasta

You would typically run the command line with clustalw_cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='clustalw', **kwargs): Initialize the class.

property align

Do full multiple alignment.

This property controls the addition of the -align switch, treat this property as a boolean.

property bootlabels

Node OR branch position of bootstrap values in tree display

This controls the addition of the -bootlabels parameter and its associated value. Set this property to the argument value required.

property bootstrap

Bootstrap a NJ tree (n= number of bootstraps; def. = 1000).

This controls the addition of the -bootstrap parameter and its associated value. Set this property to the argument value required.

property case

LOWER or UPPER (for GDE output only)

This controls the addition of the -case parameter and its associated value. Set this property to the argument value required.

property check

Outline the command line params.

This property controls the addition of the -check switch, treat this property as a boolean.

property clustering

NJ or UPGMA

This controls the addition of the -clustering parameter and its associated value. Set this property to the argument value required.

property convert

Output the input sequences in a different file format.

This property controls the addition of the -convert switch, treat this property as a boolean.

property dnamatrix

DNA weight matrix=IUB, CLUSTALW or filename

This controls the addition of the -dnamatrix parameter and its associated value. Set this property to the argument value required.

property endgaps

No end gap separation pen.

This property controls the addition of the -endgaps switch, treat this property as a boolean.

property fullhelp

Output full help content.

This property controls the addition of the -fullhelp switch, treat this property as a boolean.

property gapdist

Gap separation pen. range

This controls the addition of the -gapdist parameter and its associated value. Set this property to the argument value required.

property gapext

Gap extension penalty

This controls the addition of the -gapext parameter and its associated value. Set this property to the argument value required.

property gapopen

Gap opening penalty

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property helixendin

Number of residues inside helix to be treated as terminal

This controls the addition of the -helixendin parameter and its associated value. Set this property to the argument value required.

property helixendout

Number of residues outside helix to be treated as terminal

This controls the addition of the -helixendout parameter and its associated value. Set this property to the argument value required.

property helixgap

Gap penalty for helix core residues

This controls the addition of the -helixgap parameter and its associated value. Set this property to the argument value required.

property help

Outline the command line params.

This property controls the addition of the -help switch, treat this property as a boolean.

property hgapresidues

List hydrophilic res.

This property controls the addition of the -hgapresidues switch, treat this property as a boolean.

property infile

Input sequences.

This controls the addition of the -infile parameter and its associated value. Set this property to the argument value required.

property iteration

NONE or TREE or ALIGNMENT

This controls the addition of the -iteration parameter and its associated value. Set this property to the argument value required.

property kimura

Use Kimura’s correction.

This property controls the addition of the -kimura switch, treat this property as a boolean.

property ktuple

Word size

This controls the addition of the -ktuple parameter and its associated value. Set this property to the argument value required.

property loopgap

Gap penalty for loop regions

This controls the addition of the -loopgap parameter and its associated value. Set this property to the argument value required.

property matrix

Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename

This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

property maxdiv

% ident. for delay

This controls the addition of the -maxdiv parameter and its associated value. Set this property to the argument value required.

property maxseqlen

Maximum allowed input sequence length

This controls the addition of the -maxseqlen parameter and its associated value. Set this property to the argument value required.

property negative

Protein alignment with negative values in matrix

This property controls the addition of the -negative switch, treat this property as a boolean.

property newtree

Output file name for newly created guide tree

This controls the addition of the -newtree parameter and its associated value. Set this property to the argument value required.

property newtree1

Output file name for new guide tree of profile1

This controls the addition of the -newtree1 parameter and its associated value. Set this property to the argument value required.

property newtree2

Output file for new guide tree of profile2

This controls the addition of the -newtree2 parameter and its associated value. Set this property to the argument value required.

property nohgap

Hydrophilic gaps off

This property controls the addition of the -nohgap switch, treat this property as a boolean.

property nopgap

Residue-specific gaps off

This property controls the addition of the -nopgap switch, treat this property as a boolean.

property nosecstr1

Do not use secondary structure-gap penalty mask for profile 1

This property controls the addition of the -nosecstr1 switch, treat this property as a boolean.

property nosecstr2

Do not use secondary structure-gap penalty mask for profile 2

This property controls the addition of the -nosecstr2 switch, treat this property as a boolean.

property noweights

Disable sequence weighting

This property controls the addition of the -noweights switch, treat this property as a boolean.

property numiter

maximum number of iterations to perform

This controls the addition of the -numiter parameter and its associated value. Set this property to the argument value required.

property options

List the command line parameters

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output sequence alignment file name

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property outorder

Output taxon order: INPUT or ALIGNED

This controls the addition of the -outorder parameter and its associated value. Set this property to the argument value required.

property output

Output format: CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA

This controls the addition of the -output parameter and its associated value. Set this property to the argument value required.

property outputtree

nj OR phylip OR dist OR nexus

This controls the addition of the -outputtree parameter and its associated value. Set this property to the argument value required.

property pairgap

Gap penalty

This controls the addition of the -pairgap parameter and its associated value. Set this property to the argument value required.

property pim

Output percent identity matrix (while calculating the tree).

This property controls the addition of the -pim switch, treat this property as a boolean.

property profile

Merge two alignments by profile alignment

This property controls the addition of the -profile switch, treat this property as a boolean.

property profile1

Profiles (old alignment).

This controls the addition of the -profile1 parameter and its associated value. Set this property to the argument value required.

property profile2

Profiles (old alignment).

This controls the addition of the -profile2 parameter and its associated value. Set this property to the argument value required.

property pwdnamatrix

DNA weight matrix=IUB, CLUSTALW or filename

This controls the addition of the -pwdnamatrix parameter and its associated value. Set this property to the argument value required.

property pwgapext

Gap extension penalty

This controls the addition of the -pwgapext parameter and its associated value. Set this property to the argument value required.

property pwgapopen

Gap opening penalty

This controls the addition of the -pwgapopen parameter and its associated value. Set this property to the argument value required.

property pwmatrix

Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename

This controls the addition of the -pwmatrix parameter and its associated value. Set this property to the argument value required.

property quicktree

Use FAST algorithm for the alignment guide tree

This property controls the addition of the -quicktree switch, treat this property as a boolean.

property quiet

Reduce console output to minimum

This property controls the addition of the -quiet switch, treat this property as a boolean.

property range

Sequence range to write starting m to m+n. Input as string eg. ‘24,200’

This controls the addition of the -range parameter and its associated value. Set this property to the argument value required.

property score

Either: PERCENT or ABSOLUTE

This controls the addition of the -score parameter and its associated value. Set this property to the argument value required.

property secstrout

STRUCTURE or MASK or BOTH or NONE output in alignment file

This controls the addition of the -secstrout parameter and its associated value. Set this property to the argument value required.

property seed

Seed number for bootstraps.

This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

property seqno_range

OFF or ON (NEW- for all output formats)

This controls the addition of the -seqno_range parameter and its associated value. Set this property to the argument value required.

property seqnos

OFF or ON (for Clustal output only)

This controls the addition of the -seqnos parameter and its associated value. Set this property to the argument value required.

property sequences

Sequentially add profile2 sequences to profile1 alignment

This property controls the addition of the -sequences switch, treat this property as a boolean.

property stats

Log some alignment statistics to file

This controls the addition of the -stats parameter and its associated value. Set this property to the argument value required.

property strandendin

Number of residues inside strand to be treated as terminal

This controls the addition of the -strandendin parameter and its associated value. Set this property to the argument value required.

property strandendout

Number of residues outside strand to be treated as terminal

This controls the addition of the -strandendout parameter and its associated value. Set this property to the argument value required.

property strandgap

gap penalty for strand core residues

This controls the addition of the -strandgap parameter and its associated value. Set this property to the argument value required.

property terminalgap

Gap penalty for structure termini

This controls the addition of the -terminalgap parameter and its associated value. Set this property to the argument value required.

property topdiags

Number of best diags.

This controls the addition of the -topdiags parameter and its associated value. Set this property to the argument value required.

property tossgaps

Ignore positions with gaps.

This property controls the addition of the -tossgaps switch, treat this property as a boolean.

property transweight

Transitions weighting

This controls the addition of the -transweight parameter and its associated value. Set this property to the argument value required.

property tree

Calculate NJ tree.

This property controls the addition of the -tree switch, treat this property as a boolean.

property type

PROTEIN or DNA sequences

This controls the addition of the -type parameter and its associated value. Set this property to the argument value required.

property usetree

File name of guide tree

This controls the addition of the -usetree parameter and its associated value. Set this property to the argument value required.

property usetree1

File name of guide tree for profile1

This controls the addition of the -usetree1 parameter and its associated value. Set this property to the argument value required.

property usetree2

File name of guide tree for profile2

This controls the addition of the -usetree2 parameter and its associated value. Set this property to the argument value required.

property window

Window around best diags.

This controls the addition of the -window parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.ClustalOmegaCommandline(cmd='clustalo', **kwargs)

Bases: AbstractCommandline

Command line wrapper for clustal omega.

http://www.clustal.org/omega

Notes

Last checked against version: 1.2.0

References

Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 https://doi.org/10.1038/msb.2011.75

Examples

>>> from Bio.Align.Applications import ClustalOmegaCommandline
>>> in_file = "unaligned.fasta"
>>> out_file = "aligned.fasta"
>>> clustalomega_cline = ClustalOmegaCommandline(infile=in_file, outfile=out_file, verbose=True, auto=True)
>>> print(clustalomega_cline)
clustalo -i unaligned.fasta -o aligned.fasta --auto -v

You would typically run the command line with clustalomega_cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='clustalo', **kwargs): Initialize the class.

property auto

Set options automatically (might overwrite some of your options)

This property controls the addition of the –auto switch, treat this property as a boolean.

property clusteringout

Clustering output file

This controls the addition of the –clustering-out parameter and its associated value. Set this property to the argument value required.

property clustersize

soft maximum of sequences in sub-clusters

This controls the addition of the –cluster-size parameter and its associated value. Set this property to the argument value required.

property dealign

Dealign input sequences

This property controls the addition of the –dealign switch, treat this property as a boolean.

property distmat_full

Use full distance matrix for guide-tree calculation (slow; mBed is default)

This property controls the addition of the –full switch, treat this property as a boolean.

property distmat_full_iter

Use full distance matrix for guide-tree calculation during iteration (mBed is default)

This property controls the addition of the –full-iter switch, treat this property as a boolean.

property distmat_in

Pairwise distance matrix input file (skips distance computation).

This controls the addition of the –distmat-in parameter and its associated value. Set this property to the argument value required.

property distmat_out

Pairwise distance matrix output file.

This controls the addition of the –distmat-out parameter and its associated value. Set this property to the argument value required.

property force

Force file overwriting.

This property controls the addition of the –force switch, treat this property as a boolean.

property guidetree_in

Guide tree input file (skips distance computation and guide-tree clustering step).

This controls the addition of the –guidetree-in parameter and its associated value. Set this property to the argument value required.

property guidetree_out

Guide tree output file.

This controls the addition of the –guidetree-out parameter and its associated value. Set this property to the argument value required.

property help

Print help and exit.

This property controls the addition of the -h switch, treat this property as a boolean.

property hmm_input

HMM input files

This controls the addition of the –hmm-in parameter and its associated value. Set this property to the argument value required.

property infile

Multiple sequence input file

This controls the addition of the -i parameter and its associated value. Set this property to the argument value required.

property infmt

Forced sequence input file format (default: auto)

Allowed values: a2m, fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]

This controls the addition of the –infmt parameter and its associated value. Set this property to the argument value required.

property isprofile

disable check if profile, force profile (default no)

This property controls the addition of the –is-profile switch, treat this property as a boolean.

property iterations

Number of (combined guide-tree/HMM) iterations

This controls the addition of the –iterations parameter and its associated value. Set this property to the argument value required.

property log

Log all non-essential output to this file.

This controls the addition of the -l parameter and its associated value. Set this property to the argument value required.

property long_version

Print long version information and exit

This property controls the addition of the –long-version switch, treat this property as a boolean.

property max_guidetree_iterations

Maximum number of guidetree iterations

This controls the addition of the –max-guidetree-iterations parameter and its associated value. Set this property to the argument value required.

property max_hmm_iterations

Maximum number of HMM iterations

This controls the addition of the –max-hmm-iterations parameter and its associated value. Set this property to the argument value required.

property maxnumseq

Maximum allowed number of sequences

This controls the addition of the –maxnumseq parameter and its associated value. Set this property to the argument value required.

property maxseqlen

Maximum allowed sequence length

This controls the addition of the –maxseqlen parameter and its associated value. Set this property to the argument value required.

property outfile

Multiple sequence alignment output file (default: stdout).

This controls the addition of the -o parameter and its associated value. Set this property to the argument value required.

property outfmt

MSA output file format: a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna] (default: fasta).

This controls the addition of the –outfmt parameter and its associated value. Set this property to the argument value required.

property outputorder

MSA output order like in input/guide-tree

This controls the addition of the –output-order parameter and its associated value. Set this property to the argument value required.

property percentid

convert distances into percent identities (default no)

This property controls the addition of the –percent-id switch, treat this property as a boolean.

property profile1

Pre-aligned multiple sequence file (aligned columns will be kept fix).

This controls the addition of the –profile1 parameter and its associated value. Set this property to the argument value required.

property profile2

Pre-aligned multiple sequence file (aligned columns will be kept fix).

This controls the addition of the –profile2 parameter and its associated value. Set this property to the argument value required.

property residuenumber

in Clustal format print residue numbers (default no)

This property controls the addition of the –residuenumber switch, treat this property as a boolean.

property seqtype

{Protein, RNA, DNA} Force a sequence type (default: auto).

This controls the addition of the -t parameter and its associated value. Set this property to the argument value required.

property threads

Number of processors to use

This controls the addition of the –threads parameter and its associated value. Set this property to the argument value required.

property usekimura

use Kimura distance correction for aligned sequences (default no)

This property controls the addition of the –use-kimura switch, treat this property as a boolean.

property verbose

Verbose output

This property controls the addition of the -v switch, treat this property as a boolean.

property version

Print version information and exit

This property controls the addition of the –version switch, treat this property as a boolean.

property wrap

number of residues before line-wrap in output

This controls the addition of the –wrap parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.PrankCommandline(cmd='prank', **kwargs)

Bases: AbstractCommandline

Command line wrapper for the multiple alignment program PRANK.

http://www.ebi.ac.uk/goldman-srv/prank/prank/

Notes

Last checked against version: 081202

References

Loytynoja, A. and Goldman, N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences, 102: 10557–10562.

Loytynoja, A. and Goldman, N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320: 1632.

Examples

To align a FASTA file (unaligned.fasta) with the output in aligned FASTA format with the output filename starting with “aligned” (you can’t pick the filename explicitly), no tree output and no XML output, use:

>>> from Bio.Align.Applications import PrankCommandline
>>> prank_cline = PrankCommandline(d="unaligned.fasta",
...                                o="aligned", # prefix only!
...                                f=8, # FASTA output
...                                notree=True, noxml=True)
>>> print(prank_cline)
prank -d=unaligned.fasta -o=aligned -f=8 -noxml -notree

You would typically run the command line with prank_cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='prank', **kwargs): Initialize the class.

property F

Force insertions to be always skipped: same as +F

This property controls the addition of the -F switch, treat this property as a boolean.

property codon

Codon aware alignment or not

This property controls the addition of the -codon switch, treat this property as a boolean.

property convert

Convert input alignment to new format. Do not perform alignment

This property controls the addition of the -convert switch, treat this property as a boolean.

property d

Input filename

This controls the addition of the -d parameter and its associated value. Set this property to the argument value required.

property dnafreqs

DNA frequencies - ‘A,C,G,T’. eg ‘25,25,25,25’ as a quote surrounded string value. Default: empirical

This controls the addition of the -dnafreqs parameter and its associated value. Set this property to the argument value required.

property dots

Show insertion gaps as dots

This property controls the addition of the -dots switch, treat this property as a boolean.

property f

Output alignment format. Default: 8 FASTA Option are: 1. IG/Stanford 8. Pearson/Fasta 2. GenBank/GB 11. Phylip3.2 3. NBRF 12. Phylip 4. EMBL 14. PIR/CODATA 6. DNAStrider 15. MSF 7. Fitch 17. PAUP/NEXUS

This controls the addition of the -f parameter and its associated value. Set this property to the argument value required.

property fixedbranches

Use fixed branch lengths of input value

This controls the addition of the -fixedbranches parameter and its associated value. Set this property to the argument value required.

property gapext

Gap extension probability. Default: dna 0.5 / prot 0.5

This controls the addition of the -gapext parameter and its associated value. Set this property to the argument value required.

property gaprate

Gap opening rate. Default: dna 0.025 prot 0.0025

This controls the addition of the -gaprate parameter and its associated value. Set this property to the argument value required.

property kappa

Transition/transversion ratio. Default: 2

This controls the addition of the -kappa parameter and its associated value. Set this property to the argument value required.

property longseq

Save space in pairwise alignments

This property controls the addition of the -longseq switch, treat this property as a boolean.

property m

User-defined alignment model filename. Default: HKY2/WAG

This controls the addition of the -m parameter and its associated value. Set this property to the argument value required.

property matinitsize

Matrix initial size multiplier

This controls the addition of the -matinitsize parameter and its associated value. Set this property to the argument value required.

property matresize

Matrix resizing multiplier

This controls the addition of the -matresize parameter and its associated value. Set this property to the argument value required.

property maxbranches

Use maximum branch lengths of input value

This controls the addition of the -maxbranches parameter and its associated value. Set this property to the argument value required.

property mttranslate

Translate to protein using mt table

This property controls the addition of the -mttranslate switch, treat this property as a boolean.

property nopost

Do not compute posterior support. Default: compute

This property controls the addition of the -nopost switch, treat this property as a boolean.

property notree

Do not output dnd tree files (PRANK versions earlier than v.120626)

This property controls the addition of the -notree switch, treat this property as a boolean.

property noxml

Do not output XML files (PRANK versions earlier than v.120626)

This property controls the addition of the -noxml switch, treat this property as a boolean.

property o

Output filenames prefix. Default: ‘output’: Will write: output.?.fas (depending on requested format), output.?.xml and output.?.dnd

This controls the addition of the -o parameter and its associated value. Set this property to the argument value required.

property once

Run only once. Default: twice if no guidetree given

This property controls the addition of the -once switch, treat this property as a boolean.

property printnodes

Output each node; mostly for debugging

This property controls the addition of the -printnodes switch, treat this property as a boolean.

property pwdist

Expected pairwise distance for computing guidetree. Default: dna 0.25 / prot 0.5

This controls the addition of the -pwdist parameter and its associated value. Set this property to the argument value required.

property pwgenomic

Do pairwise alignment, no guidetree

This property controls the addition of the -pwgenomic switch, treat this property as a boolean.

property pwgenomicdist

Distance for pairwise alignment. Default: 0.3

This controls the addition of the -pwgenomicdist parameter and its associated value. Set this property to the argument value required.

property quiet

Reduce verbosity

This property controls the addition of the -quiet switch, treat this property as a boolean.

property realbranches

Disable branch length truncation

This property controls the addition of the -realbranches switch, treat this property as a boolean.

property rho

Purine/pyrimidine ratio. Default: 1

This controls the addition of the -rho parameter and its associated value. Set this property to the argument value required.

property scalebranches

Scale branch lengths. Default: dna 1 / prot 2

This controls the addition of the -scalebranches parameter and its associated value. Set this property to the argument value required.

property shortnames

Truncate names at first space

This property controls the addition of the -shortnames switch, treat this property as a boolean.

property showtree

Output dnd tree files (PRANK v.120626 and later)

This property controls the addition of the -showtree switch, treat this property as a boolean.

property showxml

Output XML files (PRANK v.120626 and later)

This property controls the addition of the -showxml switch, treat this property as a boolean.

property skipins

Skip insertions in posterior support

This property controls the addition of the -skipins switch, treat this property as a boolean.

property t

Input guide tree filename

This controls the addition of the -t parameter and its associated value. Set this property to the argument value required.

property termgap

Penalise terminal gaps normally

This property controls the addition of the -termgap switch, treat this property as a boolean.

property translate

Translate to protein

This property controls the addition of the -translate switch, treat this property as a boolean.

property tree

Input guide tree as Newick string

This controls the addition of the -tree parameter and its associated value. Set this property to the argument value required.

property twice

Always run twice

This property controls the addition of the -twice switch, treat this property as a boolean.

property uselogs

Slower but should work for a greater number of sequences

This property controls the addition of the -uselogs switch, treat this property as a boolean.

property writeanc

Output ancestral sequences

This property controls the addition of the -writeanc switch, treat this property as a boolean.

class Bio.Align.Applications.MafftCommandline(cmd='mafft', **kwargs)

Bases: AbstractCommandline

Command line wrapper for the multiple alignment program MAFFT.

http://align.bmr.kyushu-u.ac.jp/mafft/software/

Notes

Last checked against version: MAFFT v6.717b (2009/12/03)

References

Katoh, Toh (BMC Bioinformatics 9:212, 2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (describes RNA structural alignment methods)

Katoh, Toh (Briefings in Bioinformatics 9:286-298, 2008) Recent developments in the MAFFT multiple sequence alignment program (outlines version 6)

Katoh, Toh (Bioinformatics 23:372-374, 2007) Errata PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm)

Katoh, Kuma, Toh, Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)

Katoh, Misawa, Kuma, Miyata (Nucleic Acids Res. 30:3059-3066, 2002)

Examples

>>> from Bio.Align.Applications import MafftCommandline
>>> mafft_exe = "/opt/local/mafft"
>>> in_file = "../Doc/examples/opuntia.fasta"
>>> mafft_cline = MafftCommandline(mafft_exe, input=in_file)
>>> print(mafft_cline)
/opt/local/mafft ../Doc/examples/opuntia.fasta

If the mafft binary is on the path (typically the case on a Unix style operating system) then you don’t need to supply the executable location:

>>> from Bio.Align.Applications import MafftCommandline
>>> in_file = "../Doc/examples/opuntia.fasta"
>>> mafft_cline = MafftCommandline(input=in_file)
>>> print(mafft_cline)
mafft ../Doc/examples/opuntia.fasta

You would typically run the command line with mafft_cline() or via the Python subprocess module, as described in the Biopython tutorial.

Note that MAFFT will write the alignment to stdout, which you may want to save to a file and then parse, e.g.:

stdout, stderr = mafft_cline()
with open("aligned.fasta", "w") as handle:
    handle.write(stdout)
from Bio import AlignIO
align = AlignIO.read("aligned.fasta", "fasta")

Alternatively, to parse the output with AlignIO directly you can use StringIO to turn the string into a handle:

stdout, stderr = mafft_cline()
from io import StringIO
from Bio import AlignIO
align = AlignIO.read(StringIO(stdout), "fasta")

__init__(cmd='mafft', **kwargs): Initialize the class.

property LEXP

Gap extension penalty to skip the alignment. Default: 0.00

This controls the addition of the –LEXP parameter and its associated value. Set this property to the argument value required.

property LOP

Gap opening penalty to skip the alignment. Default: -6.00

This controls the addition of the –LOP parameter and its associated value. Set this property to the argument value required.

property aamatrix

Use a user-defined AA scoring matrix. Default: BLOSUM62

This controls the addition of the –aamatrix parameter and its associated value. Set this property to the argument value required.

property adjustdirection

Adjust direction according to the first sequence. Default off.

This property controls the addition of the –adjustdirection switch, treat this property as a boolean.

property adjustdirectionaccurately

Adjust direction according to the first sequence,for highly diverged data; very slowDefault off.

This property controls the addition of the –adjustdirectionaccurately switch, treat this property as a boolean.

property amino

Assume the sequences are amino acid (True/False). Default: auto

This property controls the addition of the –amino switch, treat this property as a boolean.

property auto

Automatically select strategy. Default off.

This property controls the addition of the –auto switch, treat this property as a boolean.

property bl

BLOSUM number matrix is used. Default: 62

This controls the addition of the –bl parameter and its associated value. Set this property to the argument value required.

property clustalout

Output format: clustal (True) or fasta (False, default)

This property controls the addition of the –clustalout switch, treat this property as a boolean.

property dpparttree

The PartTree algorithm is used with distances based on DP. Default: off

This property controls the addition of the –dpparttree switch, treat this property as a boolean.

property ep

Offset value, which works like gap extension penalty, for group-to- group alignment. Default: 0.123

This controls the addition of the –ep parameter and its associated value. Set this property to the argument value required.

property fastapair

All pairwise alignments are computed with FASTA (Pearson and Lipman 1988). Default: off

This property controls the addition of the –fastapair switch, treat this property as a boolean.

property fastaparttree

The PartTree algorithm is used with distances based on FASTA. Default: off

This property controls the addition of the –fastaparttree switch, treat this property as a boolean.

property fft

Use FFT approximation in group-to-group alignment. Default: on

This property controls the addition of the –fft switch, treat this property as a boolean.

property fmodel

Incorporate the AA/nuc composition information into the scoring matrix (True) or not (False, default)

This property controls the addition of the –fmodel switch, treat this property as a boolean.

property genafpair

All pairwise alignments are computed with a local algorithm with the generalized affine gap cost (Altschul 1998). Default: off

This property controls the addition of the –genafpair switch, treat this property as a boolean.

property globalpair

All pairwise alignments are computed with the Needleman-Wunsch algorithm. Default: off

This property controls the addition of the –globalpair switch, treat this property as a boolean.

property groupsize

Do not make alignment larger than number sequences. Default: the number of input sequences

This property controls the addition of the –groupsize switch, treat this property as a boolean.

property input

Input file name

This controls the addition of the input parameter and its associated value. Set this property to the argument value required.

property input1

Second input file name for the mafft-profile command

This controls the addition of the input1 parameter and its associated value. Set this property to the argument value required.

property inputorder

Output order: same as input (True, default) or alignment based (False)

This property controls the addition of the –inputorder switch, treat this property as a boolean.

property jtt

JTT PAM number (Jones et al. 1992) matrix is used. number>0. Default: BLOSUM62

This controls the addition of the –jtt parameter and its associated value. Set this property to the argument value required.

property lep

Offset value at local pairwise alignment. Default: 0.1

This controls the addition of the –lep parameter and its associated value. Set this property to the argument value required.

property lexp

Gap extension penalty at local pairwise alignment. Default: -0.1

This controls the addition of the –lexp parameter and its associated value. Set this property to the argument value required.

property localpair

All pairwise alignments are computed with the Smith-Waterman algorithm. Default: off

This property controls the addition of the –localpair switch, treat this property as a boolean.

property lop

Gap opening penalty at local pairwise alignment. Default: 0.123

This controls the addition of the –lop parameter and its associated value. Set this property to the argument value required.

property maxiterate

Number cycles of iterative refinement are performed. Default: 0

This controls the addition of the –maxiterate parameter and its associated value. Set this property to the argument value required.

property memsave

Use the Myers-Miller (1988) algorithm. Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt).

This property controls the addition of the –memsave switch, treat this property as a boolean.

property namelength

Name length in CLUSTAL and PHYLIP output.

MAFFT v6.847 (2011) added –namelength for use with the –clustalout option for CLUSTAL output.

MAFFT v7.024 (2013) added support for this with the –phylipout option for PHYLIP output (default 10).

This controls the addition of the –namelength parameter and its associated value. Set this property to the argument value required.

property nofft

Do not use FFT approximation in group-to-group alignment. Default: off

This property controls the addition of the –nofft switch, treat this property as a boolean.

property noscore

Alignment score is not checked in the iterative refinement stage. Default: off (score is checked)

This property controls the addition of the –noscore switch, treat this property as a boolean.

property nuc

Assume the sequences are nucleotide (True/False). Default: auto

This property controls the addition of the –nuc switch, treat this property as a boolean.

property op

Gap opening penalty at group-to-group alignment. Default: 1.53

This controls the addition of the –op parameter and its associated value. Set this property to the argument value required.

property partsize

The number of partitions in the PartTree algorithm. Default: 50

This controls the addition of the –partsize parameter and its associated value. Set this property to the argument value required.

property parttree

Use a fast tree-building method with the 6mer distance. Default: off

This property controls the addition of the –parttree switch, treat this property as a boolean.

property phylipout

Output format: phylip (True), or fasta (False, default)

This property controls the addition of the –phylipout switch, treat this property as a boolean.

property quiet

Do not report progress (True) or not (False, default).

This property controls the addition of the –quiet switch, treat this property as a boolean.

property reorder

Output order: aligned (True) or in input order (False, default)

This property controls the addition of the –reorder switch, treat this property as a boolean.

property retree

Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2

This controls the addition of the –retree parameter and its associated value. Set this property to the argument value required.

property seed

Seed alignments given in alignment_n (fasta format) are aligned with sequences in input.

This controls the addition of the –seed parameter and its associated value. Set this property to the argument value required.

property sixmerpair

Distance is calculated based on the number of shared 6mers. Default: on

This property controls the addition of the –6merpair switch, treat this property as a boolean.

property thread

Number of threads to use. Default: 1

This controls the addition of the –thread parameter and its associated value. Set this property to the argument value required.

property tm

Transmembrane PAM number (Jones et al. 1994) matrix is used. number>0. Default: BLOSUM62

This controls the addition of the –tm parameter and its associated value. Set this property to the argument value required.

property treeout

Guide tree is output to the input.tree file (True) or not (False, default)

This property controls the addition of the –treeout switch, treat this property as a boolean.

property weighti

Weighting factor for the consistency term calculated from pairwise alignments. Default: 2.7

This controls the addition of the –weighti parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.DialignCommandline(cmd='dialign2-2', **kwargs)

Bases: AbstractCommandline

Command line wrapper for the multiple alignment program DIALIGN2-2.

http://bibiserv.techfak.uni-bielefeld.de/dialign/welcome.html

Notes

Last checked against version: 2.2

References

B. Morgenstern (2004). DIALIGN: Multiple DNA and Protein Sequence Alignment at BiBiServ. Nucleic Acids Research 32, W33-W36.

Examples

To align a FASTA file (unaligned.fasta) with the output files names aligned.* including a FASTA output file (aligned.fa), use:

>>> from Bio.Align.Applications import DialignCommandline
>>> dialign_cline = DialignCommandline(input="unaligned.fasta",
...                                    fn="aligned", fa=True)
>>> print(dialign_cline)
dialign2-2 -fa -fn aligned unaligned.fasta

You would typically run the command line with dialign_cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='dialign2-2', **kwargs): Initialize the class.

property afc

Creates additional output file ‘*.afc’ containing data of all fragments considered for alignment WARNING: this file can be HUGE !

This property controls the addition of the -afc switch, treat this property as a boolean.

property afc_v

Like ‘-afc’ but verbose: fragments are explicitly printed. WARNING: this file can be EVEN BIGGER !

This property controls the addition of the -afc_v switch, treat this property as a boolean.

property anc

Anchored alignment. Requires a file <seq_file>.anc containing anchor points.

This property controls the addition of the -anc switch, treat this property as a boolean.

property cs

If segments are translated, not only the ‘Watson strand’ but also the ‘Crick strand’ is looked at.

This property controls the addition of the -cs switch, treat this property as a boolean.

property cw

Additional output file in CLUSTAL W format.

This property controls the addition of the -cw switch, treat this property as a boolean.

property ds

‘dna alignment speed up’ - non-translated nucleic acid fragments are taken into account only if they start with at least two matches. Speeds up DNA alignment at the expense of sensitivity.

This property controls the addition of the -ds switch, treat this property as a boolean.

property fa

Additional output file in FASTA format.

This property controls the addition of the -fa switch, treat this property as a boolean.

property ff

Creates file *.frg containing information about all fragments that are part of the respective optimal pairwise alignmnets plus information about consistency in the multiple alignment

This property controls the addition of the -ff switch, treat this property as a boolean.

property fn

Output files are named <out_file>.<extension>.

This controls the addition of the -fn parameter and its associated value. Set this property to the argument value required.

property fop

Creates file *.fop containing coordinates of all fragments that are part of the respective pairwise alignments.

This property controls the addition of the -fop switch, treat this property as a boolean.

property fsm

Creates file *.fsm containing coordinates of all fragments that are part of the final alignment

This property controls the addition of the -fsm switch, treat this property as a boolean.

property input

Input file name. Must be FASTA format

This controls the addition of the input parameter and its associated value. Set this property to the argument value required.

property iw

Overlap weights switched off (by default, overlap weights are used if up to 35 sequences are aligned). This option speeds up the alignment but may lead to reduced alignment quality.

This property controls the addition of the -iw switch, treat this property as a boolean.

property lgs

‘long genomic sequences’ - combines the following options: -ma, -thr 2, -lmax 30, -smin 8, -nta, -ff, -fop, -ff, -cs, -ds, -pst

This property controls the addition of the -lgs switch, treat this property as a boolean.

property lgs_t

Like ‘-lgs’ but with all segment pairs assessed at the peptide level (rather than ‘mixed alignments’ as with the ‘-lgs’ option). Therefore faster than -lgs but not very sensitive for non-coding regions.

This property controls the addition of the -lgs_t switch, treat this property as a boolean.

property lmax

Maximum fragment length = x (default: x = 40 or x = 120 for ‘translated’ fragments). Shorter x speeds up the program but may affect alignment quality.

This controls the addition of the -lmax parameter and its associated value. Set this property to the argument value required.

property lo

(Long Output) Additional file *.log with information about fragments selected for pairwise alignment and about consistency in multi-alignment procedure.

This property controls the addition of the -lo switch, treat this property as a boolean.

property ma

‘mixed alignments’ consisting of P-fragments and N-fragments if nucleic acid sequences are aligned.

This property controls the addition of the -ma switch, treat this property as a boolean.

property mask

Residues not belonging to selected fragments are replaced by ‘*’ characters in output alignment (rather than being printed in lower-case characters)

This property controls the addition of the -mask switch, treat this property as a boolean.

property mat

Creates file *mat with substitution counts derived from the fragments that have been selected for alignment.

This property controls the addition of the -mat switch, treat this property as a boolean.

property mat_thr

Like ‘-mat’ but only fragments with weight score > t are considered

This property controls the addition of the -mat_thr switch, treat this property as a boolean.

property max_link

‘maximum linkage’ clustering used to construct sequence tree (instead of UPGMA).

This property controls the addition of the -max_link switch, treat this property as a boolean.

property min_link

‘minimum linkage’ clustering used.

This property controls the addition of the -min_link switch, treat this property as a boolean.

property mot

‘motif’ option.

This controls the addition of the -mot parameter and its associated value. Set this property to the argument value required.

property msf

Separate output file in MSF format.

This property controls the addition of the -msf switch, treat this property as a boolean.

property n

Input sequences are nucleic acid sequences. No translation of fragments.

This property controls the addition of the -n switch, treat this property as a boolean.

property nt

Input sequences are nucleic acid sequences and ‘nucleic acid segments’ are translated to ‘peptide segments’.

This property controls the addition of the -nt switch, treat this property as a boolean.

property nta

‘no textual alignment’ - textual alignment suppressed. This option makes sense if other output files are of interest – e.g. the fragment files created with -ff, -fop, -fsm or -lo.

This property controls the addition of the -nta switch, treat this property as a boolean.

property o

Fast version, resulting alignments may be slightly different.

This property controls the addition of the -o switch, treat this property as a boolean.

property ow

Overlap weights enforced (By default, overlap weights are used only if up to 35 sequences are aligned since calculating overlap weights is time consuming).

This property controls the addition of the -ow switch, treat this property as a boolean.

property pst

‘print status’. Creates and updates a file *.sta with information about the current status of the program run. This option is recommended if large data sets are aligned since it allows the user to estimate the remaining running time.

This property controls the addition of the -pst switch, treat this property as a boolean.

property smin

Minimum similarity value for first residue pair (or codon pair) in fragments. Speeds up protein alignment or alignment of translated DNA fragments at the expense of sensitivity.

This property controls the addition of the -smin switch, treat this property as a boolean.

property stars

Maximum number of ‘*’ characters indicating degree of local similarity among sequences. By default, no stars are used but numbers between 0 and 9, instead.

This controls the addition of the -stars parameter and its associated value. Set this property to the argument value required.

property stdo

Results written to standard output.

This property controls the addition of the -stdo switch, treat this property as a boolean.

property ta

Standard textual alignment printed (overrides suppression of textual alignments in special options, e.g. -lgs)

This property controls the addition of the -ta switch, treat this property as a boolean.

property thr

Threshold T = x.

This controls the addition of the -thr parameter and its associated value. Set this property to the argument value required.

property xfr

‘exclude fragments’ - list of fragments can be specified that are NOT considered for pairwise alignment

This property controls the addition of the -xfr switch, treat this property as a boolean.

class Bio.Align.Applications.ProbconsCommandline(cmd='probcons', **kwargs)

Bases: AbstractCommandline

Command line wrapper for the multiple alignment program PROBCONS.

http://probcons.stanford.edu/

Notes

Last checked against version: 1.12

References

Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.

Examples

To align a FASTA file (unaligned.fasta) with the output in ClustalW format, and otherwise default settings, use:

>>> from Bio.Align.Applications import ProbconsCommandline
>>> probcons_cline = ProbconsCommandline(input="unaligned.fasta",
...                                      clustalw=True)
>>> print(probcons_cline)
probcons -clustalw unaligned.fasta

You would typically run the command line with probcons_cline() or via the Python subprocess module, as described in the Biopython tutorial.

Note that PROBCONS will write the alignment to stdout, which you may want to save to a file and then parse, e.g.:

stdout, stderr = probcons_cline()
with open("aligned.aln", "w") as handle:
    handle.write(stdout)
from Bio import AlignIO
align = AlignIO.read("aligned.fasta", "clustalw")

Alternatively, to parse the output with AlignIO directly you can use StringIO to turn the string into a handle:

stdout, stderr = probcons_cline()
from io import StringIO
from Bio import AlignIO
align = AlignIO.read(StringIO(stdout), "clustalw")

__init__(cmd='probcons', **kwargs): Initialize the class.

property a

Print sequences in alignment order rather than input order (default: off)

This property controls the addition of the -a switch, treat this property as a boolean.

property annot

Write annotation for multiple alignment to FILENAME

This controls the addition of the -annot parameter and its associated value. Set this property to the argument value required.

property clustalw

Use CLUSTALW output format instead of MFA

This property controls the addition of the -clustalw switch, treat this property as a boolean.

property consistency

Use 0 <= REPS <= 5 (default: 2) passes of consistency transformation

This controls the addition of the -c parameter and its associated value. Set this property to the argument value required.

property emissions

Also reestimate emission probabilities (default: off)

This property controls the addition of the -e switch, treat this property as a boolean.

property input

Input file name. Must be multiple FASTA alignment (MFA) format

This controls the addition of the input parameter and its associated value. Set this property to the argument value required.

property ir

Use 0 <= REPS <= 1000 (default: 100) passes of iterative-refinement

This controls the addition of the -ir parameter and its associated value. Set this property to the argument value required.

property pairs

Generate all-pairs pairwise alignments

This property controls the addition of the -pairs switch, treat this property as a boolean.

property paramfile

Read parameters from FILENAME

This controls the addition of the -p parameter and its associated value. Set this property to the argument value required.

property pre

Use 0 <= REPS <= 20 (default: 0) rounds of pretraining

This controls the addition of the -pre parameter and its associated value. Set this property to the argument value required.

property train

Compute EM transition probabilities, store in FILENAME (default: no training)

This controls the addition of the -t parameter and its associated value. Set this property to the argument value required.

property verbose

Report progress while aligning (default: off)

This property controls the addition of the -verbose switch, treat this property as a boolean.

property viterbi

Use Viterbi algorithm to generate all pairs (automatically enables -pairs)

This property controls the addition of the -viterbi switch, treat this property as a boolean.

class Bio.Align.Applications.TCoffeeCommandline(cmd='t_coffee', **kwargs)

Bases: AbstractCommandline

Commandline object for the TCoffee alignment program.

http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

The T-Coffee command line tool has a lot of switches and options. This wrapper implements a VERY limited number of options - if you would like to help improve it please get in touch.

Notes

Last checked against: Version_6.92

References

T-Coffee: A novel method for multiple sequence alignments. Notredame, Higgins, Heringa, JMB,302(205-217) 2000

Examples

To align a FASTA file (unaligned.fasta) with the output in ClustalW format (file aligned.aln), and otherwise default settings, use:

>>> from Bio.Align.Applications import TCoffeeCommandline
>>> tcoffee_cline = TCoffeeCommandline(infile="unaligned.fasta",
...                                    output="clustalw",
...                                    outfile="aligned.aln")
>>> print(tcoffee_cline)
t_coffee -output clustalw -infile unaligned.fasta -outfile aligned.aln

You would typically run the command line with tcoffee_cline() or via the Python subprocess module, as described in the Biopython tutorial.

SEQ_TYPES = ['dna', 'protein', 'dna_protein']

__init__(cmd='t_coffee', **kwargs): Initialize the class.

property convert

Specify you want to perform a file conversion

This property controls the addition of the -convert switch, treat this property as a boolean.

property gapext

Indicates the penalty applied for extending a gap (negative integer)

This controls the addition of the -gapext parameter and its associated value. Set this property to the argument value required.

property gapopen

Indicates the penalty applied for opening a gap (negative integer)

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property infile

Specify the input file.

This controls the addition of the -infile parameter and its associated value. Set this property to the argument value required.

property matrix

Specify the filename of the substitution matrix to use. Default: blosum62mt

This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

property mode

Specifies a special mode: genome, quickaln, dali, 3dcoffee

This controls the addition of the -mode parameter and its associated value. Set this property to the argument value required.

property outfile

Specify the output file. Default: <your sequences>.aln

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property outorder

Specify the order of sequence to outputEither ‘input’, ‘aligned’ or <filename> of Fasta file with sequence order

This controls the addition of the -outorder parameter and its associated value. Set this property to the argument value required.

property output

Specify the output type.

One (or more separated by a comma) of: ‘clustalw_aln’, ‘clustalw’, ‘gcg’, ‘msf_aln’, ‘pir_aln’, ‘fasta_aln’, ‘phylip’, ‘pir_seq’, ‘fasta_seq’

This controls the addition of the -output parameter and its associated value. Set this property to the argument value required.

property quiet

Turn off log output

This property controls the addition of the -quiet switch, treat this property as a boolean.

property type

Specify the type of sequence being aligned

This controls the addition of the -type parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.MSAProbsCommandline(cmd='msaprobs', **kwargs)

Bases: AbstractCommandline

Command line wrapper for MSAProbs.

http://msaprobs.sourceforge.net

Notes

Last checked against version: 0.9.7

References

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: “MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities”. Bioinformatics, 2010, 26(16): 1958 -1964

Examples

>>> from Bio.Align.Applications import MSAProbsCommandline
>>> in_file = "unaligned.fasta"
>>> out_file = "aligned.cla"
>>> cline = MSAProbsCommandline(infile=in_file, outfile=out_file, clustalw=True)
>>> print(cline)
msaprobs -o aligned.cla -clustalw unaligned.fasta

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(cmd='msaprobs', **kwargs): Initialize the class.

property alignment_order

print sequences in alignment order rather than input order (default: off)

This property controls the addition of the -a switch, treat this property as a boolean.

property annot

write annotation for multiple alignment to FILENAME

This controls the addition of the -annot parameter and its associated value. Set this property to the argument value required.

property clustalw

use CLUSTALW output format instead of FASTA format

This property controls the addition of the -clustalw switch, treat this property as a boolean.

property consistency

use 0 <= REPS <= 5 (default: 2) passes of consistency transformation

This controls the addition of the -c parameter and its associated value. Set this property to the argument value required.

property infile

Multiple sequence input file

This controls the addition of the infile parameter and its associated value. Set this property to the argument value required.

property iterative_refinement

use 0 <= REPS <= 1000 (default: 10) passes of iterative-refinement

This controls the addition of the -ir parameter and its associated value. Set this property to the argument value required.

property numthreads

specify the number of threads used, and otherwise detect automatically

This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

property outfile

specify the output file name (STDOUT by default)

This controls the addition of the -o parameter and its associated value. Set this property to the argument value required.

property verbose

report progress while aligning (default: off)

This property controls the addition of the -v switch, treat this property as a boolean.

property version

print out version of MSAPROBS

This controls the addition of the -version parameter and its associated value. Set this property to the argument value required.