Multiple Sequence Alignment objects

This chapter describes the older MultipleSeqAlignment class and the parsers in Bio.AlignIO that parse the output of sequence alignment software, generating MultipleSeqAlignment objects. By Multiple Sequence Alignments we mean a collection of multiple sequences which have been aligned together – usually with the insertion of gap characters, and addition of leading or trailing gaps – such that all the sequence strings are the same length. Such an alignment can be regarded as a matrix of letters, where each row is held as a SeqRecord object internally.

We will introduce the MultipleSeqAlignment object which holds this kind of data, and the Bio.AlignIO module for reading and writing them as various file formats (following the design of the Bio.SeqIO module from the previous chapter). Note that both Bio.SeqIO and Bio.AlignIO can read and write sequence alignment files. The appropriate choice will depend largely on what you want to do with the data.

The final part of this chapter is about using common multiple sequence alignment tools like ClustalW and MUSCLE from Python, and parsing the results with Biopython.

Parsing or Reading Sequence Alignments

We have two functions for reading in sequence alignments, Bio.AlignIO.read() and Bio.AlignIO.parse() which following the convention introduced in Bio.SeqIO are for files containing one or multiple alignments respectively.

Using Bio.AlignIO.parse() will return an iterator which gives MultipleSeqAlignment objects. Iterators are typically used in a for loop. Examples of situations where you will have multiple different alignments include resampled alignments from the PHYLIP tool seqboot, or multiple pairwise alignments from the EMBOSS tools water or needle, or Bill Pearson’s FASTA tools.

However, in many situations you will be dealing with files which contain only a single alignment. In this case, you should use the Bio.AlignIO.read() function which returns a single MultipleSeqAlignment object.

Both functions expect two mandatory arguments:

1. The first argument is a handle to read the data from, typically an open file (see Section What the heck is a handle?), or a filename.

2. The second argument is a lower case string specifying the alignment format. As in Bio.SeqIO we don’t try and guess the file format for you! See http://biopython.org/wiki/AlignIO for a full listing of supported formats.

There is also an optional seq_count argument which is discussed in Section Ambiguous Alignments below for dealing with ambiguous file formats which may contain more than one alignment.

Single Alignments

As an example, consider the following annotation rich protein alignment in the PFAM or Stockholm file format:

# STOCKHOLM 1.0
#=GS COATB_BPIKE/30-81  AC P03620.1
#=GS COATB_BPIKE/30-81  DR PDB; 1ifl ; 1-52;
#=GS Q9T0Q8_BPIKE/1-52  AC Q9T0Q8.1
#=GS COATB_BPI22/32-83  AC P15416.1
#=GS COATB_BPM13/24-72  AC P69541.1
#=GS COATB_BPM13/24-72  DR PDB; 2cpb ; 1-49;
#=GS COATB_BPM13/24-72  DR PDB; 2cps ; 1-49;
#=GS COATB_BPZJ2/1-49   AC P03618.1
#=GS Q9T0Q9_BPFD/1-49   AC Q9T0Q9.1
#=GS Q9T0Q9_BPFD/1-49   DR PDB; 1nh4 A; 1-49;
#=GS COATB_BPIF1/22-73  AC P03619.2
#=GS COATB_BPIF1/22-73  DR PDB; 1ifk ; 1-50;
COATB_BPIKE/30-81             AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSSKA
#=GR COATB_BPIKE/30-81  SS    -HHHHHHHHHHHHHH--HHHHHHHH--HHHHHHHHHHHHHHHHHHHHH----
Q9T0Q8_BPIKE/1-52             AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVSRA
COATB_BPI22/32-83             DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSSKA
COATB_BPM13/24-72             AEGDDP...AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA
#=GR COATB_BPM13/24-72  SS    ---S-T...CHCHHHHCCCCTCCCTTCHHHHHHHHHHHHHHHHHHHHCTT--
COATB_BPZJ2/1-49              AEGDDP...AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFASKA
Q9T0Q9_BPFD/1-49              AEGDDP...AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA
#=GR Q9T0Q9_BPFD/1-49   SS    ------...-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
COATB_BPIF1/22-73             FAADDATSQAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKLFKKFVSRA
#=GR COATB_BPIF1/22-73  SS    XX-HHHH--HHHHHH--HHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH---
#=GC SS_cons                  XHHHHHHHHHHHHHHHCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHC--
#=GC seq_cons                 AEssss...AptAhDSLpspAT-hIu.sWshVsslVsAsluIKLFKKFsSKA
//

This is the seed alignment for the Phage_Coat_Gp8 (PF05371) PFAM entry, downloaded from a now out of date release of PFAM from https://pfam.xfam.org/. We can load this file as follows (assuming it has been saved to disk as “PF05371_seed.sth” in the current working directory):

>>> from Bio import AlignIO
>>> alignment = AlignIO.read("PF05371_seed.sth", "stockholm")

This code will print out a summary of the alignment:

>>> print(alignment)
Alignment with 7 rows and 52 columns
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRL...SKA COATB_BPIKE/30-81
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKL...SRA Q9T0Q8_BPIKE/1-52
DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRL...SKA COATB_BPI22/32-83
AEGDDP---AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKL...SKA COATB_BPM13/24-72
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKL...SKA COATB_BPZJ2/1-49
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKL...SKA Q9T0Q9_BPFD/1-49
FAADDATSQAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKL...SRA COATB_BPIF1/22-73

You’ll notice in the above output the sequences have been truncated. We could instead write our own code to format this as we please by iterating over the rows as SeqRecord objects:

>>> from Bio import AlignIO
>>> alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
>>> print("Alignment length %i" % alignment.get_alignment_length())
Alignment length 52
>>> for record in alignment:
...     print("%s - %s" % (record.seq, record.id))
...
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSSKA - COATB_BPIKE/30-81
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVSRA - Q9T0Q8_BPIKE/1-52
DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSSKA - COATB_BPI22/32-83
AEGDDP---AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA - COATB_BPM13/24-72
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFASKA - COATB_BPZJ2/1-49
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA - Q9T0Q9_BPFD/1-49
FAADDATSQAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKLFKKFVSRA - COATB_BPIF1/22-73

You could also call Python’s built-in format function on the alignment object to show it in a particular file format – see Section Getting your alignment objects as formatted strings for details.

Did you notice in the raw file above that several of the sequences include database cross-references to the PDB and the associated known secondary structure? Try this:

>>> for record in alignment:
...     if record.dbxrefs:
...         print("%s %s" % (record.id, record.dbxrefs))
...
COATB_BPIKE/30-81 ['PDB; 1ifl ; 1-52;']
COATB_BPM13/24-72 ['PDB; 2cpb ; 1-49;', 'PDB; 2cps ; 1-49;']
Q9T0Q9_BPFD/1-49 ['PDB; 1nh4 A; 1-49;']
COATB_BPIF1/22-73 ['PDB; 1ifk ; 1-50;']

To have a look at all the sequence annotation, try this:

>>> for record in alignment:
...     print(record)
...

PFAM provide a nice web interface at http://pfam.xfam.org/family/PF05371 which will actually let you download this alignment in several other formats. This is what the file looks like in the FASTA file format:

>COATB_BPIKE/30-81
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSSKA
>Q9T0Q8_BPIKE/1-52
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVSRA
>COATB_BPI22/32-83
DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSSKA
>COATB_BPM13/24-72
AEGDDP---AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA
>COATB_BPZJ2/1-49
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFASKA
>Q9T0Q9_BPFD/1-49
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA
>COATB_BPIF1/22-73
FAADDATSQAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKLFKKFVSRA

Note the website should have an option about showing gaps as periods (dots) or dashes, we’ve shown dashes above. Assuming you download and save this as file “PF05371_seed.faa” then you can load it with almost exactly the same code:

>>> from Bio import AlignIO
>>> alignment = AlignIO.read("PF05371_seed.faa", "fasta")
>>> print(alignment)

All that has changed in this code is the filename and the format string. You’ll get the same output as before, the sequences and record identifiers are the same. However, as you should expect, if you check each SeqRecord there is no annotation nor database cross-references because these are not included in the FASTA file format.

Note that rather than using the Sanger website, you could have used Bio.AlignIO to convert the original Stockholm format file into a FASTA file yourself (see below).

With any supported file format, you can load an alignment in exactly the same way just by changing the format string. For example, use “phylip” for PHYLIP files, “nexus” for NEXUS files or “emboss” for the alignments output by the EMBOSS tools. There is a full listing on the wiki page (http://biopython.org/wiki/AlignIO) and in the built-in documentation, Bio.AlignIO:

>>> from Bio import AlignIO
>>> help(AlignIO)

Multiple Alignments

The previous section focused on reading files containing a single alignment. In general however, files can contain more than one alignment, and to read these files we must use the Bio.AlignIO.parse() function.

Suppose you have a small alignment in PHYLIP format:

    5    6
Alpha     AACAAC
Beta      AACCCC
Gamma     ACCAAC
Delta     CCACCA
Epsilon   CCAAAC

If you wanted to bootstrap a phylogenetic tree using the PHYLIP tools, one of the steps would be to create a set of many resampled alignments using the tool bootseq. This would give output something like this, which has been abbreviated for conciseness:

    5     6
Alpha     AAACCA
Beta      AAACCC
Gamma     ACCCCA
Delta     CCCAAC
Epsilon   CCCAAA
    5     6
Alpha     AAACAA
Beta      AAACCC
Gamma     ACCCAA
Delta     CCCACC
Epsilon   CCCAAA
    5     6
Alpha     AAAAAC
Beta      AAACCC
Gamma     AACAAC
Delta     CCCCCA
Epsilon   CCCAAC
...
    5     6
Alpha     AAAACC
Beta      ACCCCC
Gamma     AAAACC
Delta     CCCCAA
Epsilon   CAAACC

If you wanted to read this in using Bio.AlignIO you could use:

>>> from Bio import AlignIO
>>> alignments = AlignIO.parse("resampled.phy", "phylip")
>>> for alignment in alignments:
...     print(alignment)
...     print()
...

This would give the following output, again abbreviated for display:

Alignment with 5 rows and 6 columns
AAACCA Alpha
AAACCC Beta
ACCCCA Gamma
CCCAAC Delta
CCCAAA Epsilon

Alignment with 5 rows and 6 columns
AAACAA Alpha
AAACCC Beta
ACCCAA Gamma
CCCACC Delta
CCCAAA Epsilon

Alignment with 5 rows and 6 columns
AAAAAC Alpha
AAACCC Beta
AACAAC Gamma
CCCCCA Delta
CCCAAC Epsilon

...

Alignment with 5 rows and 6 columns
AAAACC Alpha
ACCCCC Beta
AAAACC Gamma
CCCCAA Delta
CAAACC Epsilon

As with the function Bio.SeqIO.parse(), using Bio.AlignIO.parse() returns an iterator. If you want to keep all the alignments in memory at once, which will allow you to access them in any order, then turn the iterator into a list:

>>> from Bio import AlignIO
>>> alignments = list(AlignIO.parse("resampled.phy", "phylip"))
>>> last_align = alignments[-1]
>>> first_align = alignments[0]

Ambiguous Alignments

Many alignment file formats can explicitly store more than one alignment, and the division between each alignment is clear. However, when a general sequence file format has been used there is no such block structure. The most common such situation is when alignments have been saved in the FASTA file format. For example consider the following:

>Alpha
ACTACGACTAGCTCAG--G
>Beta
ACTACCGCTAGCTCAGAAG
>Gamma
ACTACGGCTAGCACAGAAG
>Alpha
ACTACGACTAGCTCAGG--
>Beta
ACTACCGCTAGCTCAGAAG
>Gamma
ACTACGGCTAGCACAGAAG

This could be a single alignment containing six sequences (with repeated identifiers). Or, judging from the identifiers, this is probably two different alignments each with three sequences, which happen to all have the same length.

What about this next example?

>Alpha
ACTACGACTAGCTCAG--G
>Beta
ACTACCGCTAGCTCAGAAG
>Alpha
ACTACGACTAGCTCAGG--
>Gamma
ACTACGGCTAGCACAGAAG
>Alpha
ACTACGACTAGCTCAGG--
>Delta
ACTACGGCTAGCACAGAAG

Again, this could be a single alignment with six sequences. However this time based on the identifiers we might guess this is three pairwise alignments which by chance have all got the same lengths.

This final example is similar:

>Alpha
ACTACGACTAGCTCAG--G
>XXX
ACTACCGCTAGCTCAGAAG
>Alpha
ACTACGACTAGCTCAGG
>YYY
ACTACGGCAAGCACAGG
>Alpha
--ACTACGAC--TAGCTCAGG
>ZZZ
GGACTACGACAATAGCTCAGG

In this third example, because of the differing lengths, this cannot be treated as a single alignment containing all six records. However, it could be three pairwise alignments.

Clearly trying to store more than one alignment in a FASTA file is not ideal. However, if you are forced to deal with these as input files Bio.AlignIO can cope with the most common situation where all the alignments have the same number of records. One example of this is a collection of pairwise alignments, which can be produced by the EMBOSS tools needle and water – although in this situation, Bio.AlignIO should be able to understand their native output using “emboss” as the format string.

To interpret these FASTA examples as several separate alignments, we can use Bio.AlignIO.parse() with the optional seq_count argument which specifies how many sequences are expected in each alignment (in these examples, 3, 2 and 2 respectively). For example, using the third example as the input data:

>>> for alignment in AlignIO.parse(handle, "fasta", seq_count=2):
...     print("Alignment length %i" % alignment.get_alignment_length())
...     for record in alignment:
...         print("%s - %s" % (record.seq, record.id))
...     print()
...

giving:

Alignment length 19
ACTACGACTAGCTCAG--G - Alpha
ACTACCGCTAGCTCAGAAG - XXX

Alignment length 17
ACTACGACTAGCTCAGG - Alpha
ACTACGGCAAGCACAGG - YYY

Alignment length 21
--ACTACGAC--TAGCTCAGG - Alpha
GGACTACGACAATAGCTCAGG - ZZZ

Using Bio.AlignIO.read() or Bio.AlignIO.parse() without the seq_count argument would give a single alignment containing all six records for the first two examples. For the third example, an exception would be raised because the lengths differ preventing them being turned into a single alignment.

If the file format itself has a block structure allowing Bio.AlignIO to determine the number of sequences in each alignment directly, then the seq_count argument is not needed. If it is supplied, and doesn’t agree with the file contents, an error is raised.

Note that this optional seq_count argument assumes each alignment in the file has the same number of sequences. Hypothetically you may come across stranger situations, for example a FASTA file containing several alignments each with a different number of sequences – although I would love to hear of a real world example of this. Assuming you cannot get the data in a nicer file format, there is no straight forward way to deal with this using Bio.AlignIO. In this case, you could consider reading in the sequences themselves using Bio.SeqIO and batching them together to create the alignments as appropriate.

Writing Alignments

We’ve talked about using Bio.AlignIO.read() and Bio.AlignIO.parse() for alignment input (reading files), and now we’ll look at Bio.AlignIO.write() which is for alignment output (writing files). This is a function taking three arguments: some MultipleSeqAlignment objects (or for backwards compatibility the obsolete Alignment objects), a handle or filename to write to, and a sequence format.

Here is an example, where we start by creating a few MultipleSeqAlignment objects the hard way (by hand, rather than by loading them from a file). Note we create some SeqRecord objects to construct the alignment from.

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> from Bio.Align import MultipleSeqAlignment
>>> align1 = MultipleSeqAlignment(
...     [
...         SeqRecord(Seq("ACTGCTAGCTAG"), id="Alpha"),
...         SeqRecord(Seq("ACT-CTAGCTAG"), id="Beta"),
...         SeqRecord(Seq("ACTGCTAGDTAG"), id="Gamma"),
...     ]
... )
>>> align2 = MultipleSeqAlignment(
...     [
...         SeqRecord(Seq("GTCAGC-AG"), id="Delta"),
...         SeqRecord(Seq("GACAGCTAG"), id="Epsilon"),
...         SeqRecord(Seq("GTCAGCTAG"), id="Zeta"),
...     ]
... )
>>> align3 = MultipleSeqAlignment(
...     [
...         SeqRecord(Seq("ACTAGTACAGCTG"), id="Eta"),
...         SeqRecord(Seq("ACTAGTACAGCT-"), id="Theta"),
...         SeqRecord(Seq("-CTACTACAGGTG"), id="Iota"),
...     ]
... )
>>> my_alignments = [align1, align2, align3]

Now we have a list of Alignment objects, we’ll write them to a PHYLIP format file:

>>> from Bio import AlignIO
>>> AlignIO.write(my_alignments, "my_example.phy", "phylip")

And if you open this file in your favorite text editor it should look like this:

 3 12
Alpha      ACTGCTAGCT AG
Beta       ACT-CTAGCT AG
Gamma      ACTGCTAGDT AG
 3 9
Delta      GTCAGC-AG
Epislon    GACAGCTAG
Zeta       GTCAGCTAG
 3 13
Eta        ACTAGTACAG CTG
Theta      ACTAGTACAG CT-
Iota       -CTACTACAG GTG

Its more common to want to load an existing alignment, and save that, perhaps after some simple manipulation like removing certain rows or columns.

Suppose you wanted to know how many alignments the Bio.AlignIO.write() function wrote to the handle? If your alignments were in a list like the example above, you could just use len(my_alignments), however you can’t do that when your records come from a generator/iterator. Therefore the Bio.AlignIO.write() function returns the number of alignments written to the file.

Note - If you tell the Bio.AlignIO.write() function to write to a file that already exists, the old file will be overwritten without any warning.

Converting between sequence alignment file formats

Converting between sequence alignment file formats with Bio.AlignIO works in the same way as converting between sequence file formats with Bio.SeqIO (Section Converting between sequence file formats). We load generally the alignment(s) using Bio.AlignIO.parse() and then save them using the Bio.AlignIO.write() – or just use the Bio.AlignIO.convert() helper function.

For this example, we’ll load the PFAM/Stockholm format file used earlier and save it as a Clustal W format file:

>>> from Bio import AlignIO
>>> count = AlignIO.convert("PF05371_seed.sth", "stockholm", "PF05371_seed.aln", "clustal")
>>> print("Converted %i alignments" % count)
Converted 1 alignments

Or, using Bio.AlignIO.parse() and Bio.AlignIO.write():

>>> from Bio import AlignIO
>>> alignments = AlignIO.parse("PF05371_seed.sth", "stockholm")
>>> count = AlignIO.write(alignments, "PF05371_seed.aln", "clustal")
>>> print("Converted %i alignments" % count)
Converted 1 alignments

The Bio.AlignIO.write() function expects to be given multiple alignment objects. In the example above we gave it the alignment iterator returned by Bio.AlignIO.parse().

In this case, we know there is only one alignment in the file so we could have used Bio.AlignIO.read() instead, but notice we have to pass this alignment to Bio.AlignIO.write() as a single element list:

>>> from Bio import AlignIO
>>> alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
>>> AlignIO.write([alignment], "PF05371_seed.aln", "clustal")

Either way, you should end up with the same new Clustal W format file “PF05371_seed.aln” with the following content:

CLUSTAL X (1.81) multiple sequence alignment


COATB_BPIKE/30-81                   AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSS
Q9T0Q8_BPIKE/1-52                   AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVS
COATB_BPI22/32-83                   DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSS
COATB_BPM13/24-72                   AEGDDP---AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTS
COATB_BPZJ2/1-49                    AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFAS
Q9T0Q9_BPFD/1-49                    AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTS
COATB_BPIF1/22-73                   FAADDATSQAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKLFKKFVS

COATB_BPIKE/30-81                   KA
Q9T0Q8_BPIKE/1-52                   RA
COATB_BPI22/32-83                   KA
COATB_BPM13/24-72                   KA
COATB_BPZJ2/1-49                    KA
Q9T0Q9_BPFD/1-49                    KA
COATB_BPIF1/22-73                   RA

Alternatively, you could make a PHYLIP format file which we’ll name “PF05371_seed.phy”:

>>> from Bio import AlignIO
>>> AlignIO.convert("PF05371_seed.sth", "stockholm", "PF05371_seed.phy", "phylip")

This time the output looks like this:

 7 52
COATB_BPIK AEPNAATNYA TEAMDSLKTQ AIDLISQTWP VVTTVVVAGL VIRLFKKFSS
Q9T0Q8_BPI AEPNAATNYA TEAMDSLKTQ AIDLISQTWP VVTTVVVAGL VIKLFKKFVS
COATB_BPI2 DGTSTATSYA TEAMNSLKTQ ATDLIDQTWP VVTSVAVAGL AIRLFKKFSS
COATB_BPM1 AEGDDP---A KAAFNSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFTS
COATB_BPZJ AEGDDP---A KAAFDSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFAS
Q9T0Q9_BPF AEGDDP---A KAAFDSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFTS
COATB_BPIF FAADDATSQA KAAFDSLTAQ ATEMSGYAWA LVVLVVGATV GIKLFKKFVS

           KA
           RA
           KA
           KA
           KA
           KA
           RA

One of the big handicaps of the original PHYLIP alignment file format is that the sequence identifiers are strictly truncated at ten characters. In this example, as you can see the resulting names are still unique - but they are not very readable. As a result, a more relaxed variant of the original PHYLIP format is now quite widely used:

>>> from Bio import AlignIO
>>> AlignIO.convert("PF05371_seed.sth", "stockholm", "PF05371_seed.phy", "phylip-relaxed")

This time the output looks like this, using a longer indentation to allow all the identifiers to be given in full:

 7 52
COATB_BPIKE/30-81  AEPNAATNYA TEAMDSLKTQ AIDLISQTWP VVTTVVVAGL VIRLFKKFSS
Q9T0Q8_BPIKE/1-52  AEPNAATNYA TEAMDSLKTQ AIDLISQTWP VVTTVVVAGL VIKLFKKFVS
COATB_BPI22/32-83  DGTSTATSYA TEAMNSLKTQ ATDLIDQTWP VVTSVAVAGL AIRLFKKFSS
COATB_BPM13/24-72  AEGDDP---A KAAFNSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFTS
COATB_BPZJ2/1-49   AEGDDP---A KAAFDSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFAS
Q9T0Q9_BPFD/1-49   AEGDDP---A KAAFDSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFTS
COATB_BPIF1/22-73  FAADDATSQA KAAFDSLTAQ ATEMSGYAWA LVVLVVGATV GIKLFKKFVS

                   KA
                   RA
                   KA
                   KA
                   KA
                   KA
                   RA

If you have to work with the original strict PHYLIP format, then you may need to compress the identifiers somehow – or assign your own names or numbering system. This following bit of code manipulates the record identifiers before saving the output:

>>> from Bio import AlignIO
>>> alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
>>> name_mapping = {}
>>> for i, record in enumerate(alignment):
...     name_mapping[i] = record.id
...     record.id = "seq%i" % i
...
>>> print(name_mapping)
{0: 'COATB_BPIKE/30-81', 1: 'Q9T0Q8_BPIKE/1-52', 2: 'COATB_BPI22/32-83', 3: 'COATB_BPM13/24-72', 4: 'COATB_BPZJ2/1-49', 5: 'Q9T0Q9_BPFD/1-49', 6: 'COATB_BPIF1/22-73'}
>>> AlignIO.write([alignment], "PF05371_seed.phy", "phylip")

This code used a Python dictionary to record a simple mapping from the new sequence system to the original identifier:

{
    0: "COATB_BPIKE/30-81",
    1: "Q9T0Q8_BPIKE/1-52",
    2: "COATB_BPI22/32-83",
    # ...
}

Here is the new (strict) PHYLIP format output:

 7 52
seq0       AEPNAATNYA TEAMDSLKTQ AIDLISQTWP VVTTVVVAGL VIRLFKKFSS
seq1       AEPNAATNYA TEAMDSLKTQ AIDLISQTWP VVTTVVVAGL VIKLFKKFVS
seq2       DGTSTATSYA TEAMNSLKTQ ATDLIDQTWP VVTSVAVAGL AIRLFKKFSS
seq3       AEGDDP---A KAAFNSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFTS
seq4       AEGDDP---A KAAFDSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFAS
seq5       AEGDDP---A KAAFDSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFTS
seq6       FAADDATSQA KAAFDSLTAQ ATEMSGYAWA LVVLVVGATV GIKLFKKFVS

           KA
           RA
           KA
           KA
           KA
           KA
           RA

In general, because of the identifier limitation, working with strict PHYLIP file formats shouldn’t be your first choice. Using the PFAM/Stockholm format on the other hand allows you to record a lot of additional annotation too.

Getting your alignment objects as formatted strings

The Bio.AlignIO interface is based on handles, which means if you want to get your alignment(s) into a string in a particular file format you need to do a little bit more work (see below). However, you will probably prefer to call Python’s built-in format function on the alignment object. This takes an output format specification as a single argument, a lower case string which is supported by Bio.AlignIO as an output format. For example:

>>> from Bio import AlignIO
>>> alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
>>> print(format(alignment, "clustal"))
CLUSTAL X (1.81) multiple sequence alignment


COATB_BPIKE/30-81                   AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSS
Q9T0Q8_BPIKE/1-52                   AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVS
COATB_BPI22/32-83                   DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSS
...

Without an output format specification, format returns the same output as str.

As described in Section The format method, the SeqRecord object has a similar method using output formats supported by Bio.SeqIO.

Internally format is calling Bio.AlignIO.write() with a StringIO handle. You can do this in your own code if for example you are using an older version of Biopython:

>>> from io import StringIO
>>> from Bio import AlignIO
>>> alignments = AlignIO.parse("PF05371_seed.sth", "stockholm")
>>> out_handle = StringIO()
>>> AlignIO.write(alignments, out_handle, "clustal")
1
>>> clustal_data = out_handle.getvalue()
>>> print(clustal_data)
CLUSTAL X (1.81) multiple sequence alignment


COATB_BPIKE/30-81                   AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSS
Q9T0Q8_BPIKE/1-52                   AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVS
COATB_BPI22/32-83                   DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSS
COATB_BPM13/24-72                   AEGDDP---AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTS
...

Manipulating Alignments

Now that we’ve covered loading and saving alignments, we’ll look at what else you can do with them.

Slicing alignments

First of all, in some senses the alignment objects act like a Python list of SeqRecord objects (the rows). With this model in mind hopefully the actions of len() (the number of rows) and iteration (each row as a SeqRecord) make sense:

>>> from Bio import AlignIO
>>> alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
>>> print("Number of rows: %i" % len(alignment))
Number of rows: 7
>>> for record in alignment:
...     print("%s - %s" % (record.seq, record.id))
...
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSSKA - COATB_BPIKE/30-81
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVSRA - Q9T0Q8_BPIKE/1-52
DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSSKA - COATB_BPI22/32-83
AEGDDP---AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA - COATB_BPM13/24-72
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFASKA - COATB_BPZJ2/1-49
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA - Q9T0Q9_BPFD/1-49
FAADDATSQAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKLFKKFVSRA - COATB_BPIF1/22-73

You can also use the list-like append and extend methods to add more rows to the alignment (as SeqRecord objects). Keeping the list metaphor in mind, simple slicing of the alignment should also make sense - it selects some of the rows giving back another alignment object:

>>> print(alignment)
Alignment with 7 rows and 52 columns
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRL...SKA COATB_BPIKE/30-81
AEPNAATNYATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKL...SRA Q9T0Q8_BPIKE/1-52
DGTSTATSYATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRL...SKA COATB_BPI22/32-83
AEGDDP---AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKL...SKA COATB_BPM13/24-72
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKL...SKA COATB_BPZJ2/1-49
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKL...SKA Q9T0Q9_BPFD/1-49
FAADDATSQAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKL...SRA COATB_BPIF1/22-73
>>> print(alignment[3:7])
Alignment with 4 rows and 52 columns
AEGDDP---AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKL...SKA COATB_BPM13/24-72
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKL...SKA COATB_BPZJ2/1-49
AEGDDP---AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKL...SKA Q9T0Q9_BPFD/1-49
FAADDATSQAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKL...SRA COATB_BPIF1/22-73

What if you wanted to select by column? Those of you who have used the NumPy matrix or array objects won’t be surprised at this - you use a double index.

>>> print(alignment[2, 6])
T

Using two integer indices pulls out a single letter, short hand for this:

>>> print(alignment[2].seq[6])
T

You can pull out a single column as a string like this:

>>> print(alignment[:, 6])
TTT---T

You can also select a range of columns. For example, to pick out those same three rows we extracted earlier, but take just their first six columns:

>>> print(alignment[3:6, :6])
Alignment with 3 rows and 6 columns
AEGDDP COATB_BPM13/24-72
AEGDDP COATB_BPZJ2/1-49
AEGDDP Q9T0Q9_BPFD/1-49

Leaving the first index as : means take all the rows:

>>> print(alignment[:, :6])
Alignment with 7 rows and 6 columns
AEPNAA COATB_BPIKE/30-81
AEPNAA Q9T0Q8_BPIKE/1-52
DGTSTA COATB_BPI22/32-83
AEGDDP COATB_BPM13/24-72
AEGDDP COATB_BPZJ2/1-49
AEGDDP Q9T0Q9_BPFD/1-49
FAADDA COATB_BPIF1/22-73

This brings us to a neat way to remove a section. Notice columns 7, 8 and 9 which are gaps in three of the seven sequences:

>>> print(alignment[:, 6:9])
Alignment with 7 rows and 3 columns
TNY COATB_BPIKE/30-81
TNY Q9T0Q8_BPIKE/1-52
TSY COATB_BPI22/32-83
--- COATB_BPM13/24-72
--- COATB_BPZJ2/1-49
--- Q9T0Q9_BPFD/1-49
TSQ COATB_BPIF1/22-73

Again, you can slice to get everything after the ninth column:

>>> print(alignment[:, 9:])
Alignment with 7 rows and 43 columns
ATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSSKA COATB_BPIKE/30-81
ATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVSRA Q9T0Q8_BPIKE/1-52
ATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSSKA COATB_BPI22/32-83
AKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA COATB_BPM13/24-72
AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFASKA COATB_BPZJ2/1-49
AKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA Q9T0Q9_BPFD/1-49
AKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKLFKKFVSRA COATB_BPIF1/22-73

Now, the interesting thing is that addition of alignment objects works by column. This lets you do this as a way to remove a block of columns:

>>> edited = alignment[:, :6] + alignment[:, 9:]
>>> print(edited)
Alignment with 7 rows and 49 columns
AEPNAAATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSSKA COATB_BPIKE/30-81
AEPNAAATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVSRA Q9T0Q8_BPIKE/1-52
DGTSTAATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSSKA COATB_BPI22/32-83
AEGDDPAKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA COATB_BPM13/24-72
AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFASKA COATB_BPZJ2/1-49
AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA Q9T0Q9_BPFD/1-49
FAADDAAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKLFKKFVSRA COATB_BPIF1/22-73

Another common use of alignment addition would be to combine alignments for several different genes into a meta-alignment. Watch out though - the identifiers need to match up (see Section Adding SeqRecord objects for how adding SeqRecord objects works). You may find it helpful to first sort the alignment rows alphabetically by id:

>>> edited.sort()
>>> print(edited)
Alignment with 7 rows and 49 columns
DGTSTAATEAMNSLKTQATDLIDQTWPVVTSVAVAGLAIRLFKKFSSKA COATB_BPI22/32-83
FAADDAAKAAFDSLTAQATEMSGYAWALVVLVVGATVGIKLFKKFVSRA COATB_BPIF1/22-73
AEPNAAATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIRLFKKFSSKA COATB_BPIKE/30-81
AEGDDPAKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA COATB_BPM13/24-72
AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFASKA COATB_BPZJ2/1-49
AEPNAAATEAMDSLKTQAIDLISQTWPVVTTVVVAGLVIKLFKKFVSRA Q9T0Q8_BPIKE/1-52
AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA Q9T0Q9_BPFD/1-49

Note that you can only add two alignments together if they have the same number of rows.

Alignments as arrays

Depending on what you are doing, it can be more useful to turn the alignment object into an array of letters – and you can do this with NumPy:

>>> import numpy as np
>>> from Bio import AlignIO
>>> alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
>>> align_array = np.array(alignment)
>>> print("Array shape %i by %i" % align_array.shape)
Array shape 7 by 52
>>> align_array[:, :10]  
array([['A', 'E', 'P', 'N', 'A', 'A', 'T', 'N', 'Y', 'A'],
       ['A', 'E', 'P', 'N', 'A', 'A', 'T', 'N', 'Y', 'A'],
       ['D', 'G', 'T', 'S', 'T', 'A', 'T', 'S', 'Y', 'A'],
       ['A', 'E', 'G', 'D', 'D', 'P', '-', '-', '-', 'A'],
       ['A', 'E', 'G', 'D', 'D', 'P', '-', '-', '-', 'A'],
       ['A', 'E', 'G', 'D', 'D', 'P', '-', '-', '-', 'A'],
       ['F', 'A', 'A', 'D', 'D', 'A', 'T', 'S', 'Q', 'A']],...

Note that this leaves the original Biopython alignment object and the NumPy array in memory as separate objects - editing one will not update the other!

Counting substitutions

The substitutions property of an alignment reports how often letters in the alignment are substituted for each other. This is calculated by taking all pairs of rows in the alignment, counting the number of times two letters are aligned to each other, and summing this over all pairs. For example,

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> from Bio.Align import MultipleSeqAlignment
>>> msa = MultipleSeqAlignment(
...     [
...         SeqRecord(Seq("ACTCCTA"), id="seq1"),
...         SeqRecord(Seq("AAT-CTA"), id="seq2"),
...         SeqRecord(Seq("CCTACT-"), id="seq3"),
...         SeqRecord(Seq("TCTCCTC"), id="seq4"),
...     ]
... )
>>> print(msa)
Alignment with 4 rows and 7 columns
ACTCCTA seq1
AAT-CTA seq2
CCTACT- seq3
TCTCCTC seq4
>>> substitutions = msa.substitutions
>>> print(substitutions)
    A    C    T
A 2.0  4.5  1.0
C 4.5 10.0  0.5
T 1.0  0.5 12.0

As the ordering of pairs is arbitrary, counts are divided equally above and below the diagonal. For example, the 9 alignments of A to C are stored as 4.5 at position ['A', 'C'] and 4.5 at position ['C', 'A']. This arrangement helps to make the math easier when calculating a substitution matrix from these counts, as described in Section Substitution matrices.

Note that msa.substitutions contains entries for the letters appearing in the alignment only. You can use the select method to add entries for missing letters, for example

>>> m = substitutions.select("ATCG")
>>> print(m)
    A    T    C   G
A 2.0  1.0  4.5 0.0
T 1.0 12.0  0.5 0.0
C 4.5  0.5 10.0 0.0
G 0.0  0.0  0.0 0.0

This also allows you to change the order of letters in the alphabet.

Calculating summary information

Once you have an alignment, you are very likely going to want to find out information about it. Instead of trying to have all of the functions that can generate information about an alignment in the alignment object itself, we’ve tried to separate out the functionality into separate classes, which act on the alignment.

Getting ready to calculate summary information about an object is quick to do. Let’s say we’ve got an alignment object called alignment, for example read in using Bio.AlignIO.read(...) as described in Chapter Multiple Sequence Alignment objects. All we need to do to get an object that will calculate summary information is:

>>> from Bio.Align import AlignInfo
>>> summary_align = AlignInfo.SummaryInfo(msa)

The summary_align object is very useful, and will do the following neat things for you:

1. Calculate a quick consensus sequence – see section Calculating a quick consensus sequence

2. Get a position specific score matrix for the alignment – see section Position Specific Score Matrices

3. Calculate the information content for the alignment – see section Information Content

4. Generate information on substitutions in the alignment – section Substitution matrices details using this to generate a substitution matrix.

Calculating a quick consensus sequence

The SummaryInfo object, described in section Calculating summary information, provides functionality to calculate a quick consensus of an alignment. Assuming we’ve got a SummaryInfo object called summary_align we can calculate a consensus by doing:

>>> consensus = summary_align.dumb_consensus()
>>> consensus
Seq('XCTXCTX')

As the name suggests, this is a really simple consensus calculator, and will just add up all of the residues at each point in the consensus, and if the most common value is higher than some threshold value will add the common residue to the consensus. If it doesn’t reach the threshold, it adds an ambiguity character to the consensus. The returned consensus object is a Seq object.

You can adjust how dumb_consensus works by passing optional parameters:

the threshold

This is the threshold specifying how common a particular residue has to be at a position before it is added. The default is \(0.7\) (meaning \(70\%\)).

the ambiguous character

This is the ambiguity character to use. The default is ’N’.

Alternatively, you can convert the multiple sequence alignment object msa to a new-style Alignment object (see section Alignment objects) by using the alignment attribute (see section Getting a new-style Alignment object):

>>> alignment = msa.alignment

You can then create a Motif object (see section Motif objects):

>>> from Bio.motifs import Motif
>>> motif = Motif("ACGT", alignment)

and obtain a quick consensus sequence:

>>> motif.consensus
Seq('ACTCCTA')

The motif.counts.calculate_consensus method (see section Obtaining a consensus sequence) lets you specify in detail how the consensus sequence should be calculated. For example,

>>> motif.counts.calculate_consensus(identity=0.7)
'NCTNCTN'

Position Specific Score Matrices

Position specific score matrices (PSSMs) summarize the alignment information in a different way than a consensus, and may be useful for different tasks. Basically, a PSSM is a count matrix. For each column in the alignment, the number of each alphabet letters is counted and totaled. The totals are displayed relative to some representative sequence along the left axis. This sequence may be the consensus sequence, but can also be any sequence in the alignment.

For instance for the alignment above:

>>> print(msa)
Alignment with 4 rows and 7 columns
ACTCCTA seq1
AAT-CTA seq2
CCTACT- seq3
TCTCCTC seq4

we get a PSSM with the consensus sequence along the side using

>>> my_pssm = summary_align.pos_specific_score_matrix(consensus, chars_to_ignore=["N"])
>>> print(my_pssm)
    A   C   T
X  2.0 1.0 1.0
C  1.0 3.0 0.0
T  0.0 0.0 4.0
X  1.0 2.0 0.0
C  0.0 4.0 0.0
T  0.0 0.0 4.0
X  2.0 1.0 0.0

where we ignore any N ambiguity residues when calculating the PSSM.

Two notes should be made about this:

1. To maintain strictness with the alphabets, you can only include characters along the top of the PSSM that are in the alphabet of the alignment object. Gaps are not included along the top axis of the PSSM.

2. The sequence passed to be displayed along the left side of the axis does not need to be the consensus. For instance, if you wanted to display the second sequence in the alignment along this axis, you would need to do:

   >>> second_seq = msa[1]
   >>> my_pssm = summary_align.pos_specific_score_matrix(second_seq, chars_to_ignore=["N"])
   >>> print(my_pssm)
       A   C   T
   A  2.0 1.0 1.0
   A  1.0 3.0 0.0
   T  0.0 0.0 4.0
   -  1.0 2.0 0.0
   C  0.0 4.0 0.0
   T  0.0 0.0 4.0
   A  2.0 1.0 0.0
   

The command above returns a PSSM object. You can access any element of the PSSM by subscripting like your_pssm[sequence_number][residue_count_name]. For instance, to get the counts for the ’A’ residue in the second element of the above PSSM you would do:

>>> print(my_pssm[5]["T"])
4.0

The structure of the PSSM class hopefully makes it easy both to access elements and to pretty print the matrix.

Alternatively, you can convert the multiple sequence alignment object msa to a new-style Alignment object (see section Alignment objects) by using the alignment attribute (see section Getting a new-style Alignment object):

>>> alignment = msa.alignment

You can then create a Motif object (see section Motif objects):

>>> from Bio.motifs import Motif
>>> motif = Motif("ACGT", alignment)

and obtain the counts of each nucleotide in each position:

>>> counts = motif.counts
>>> print(counts)
        0      1      2      3      4      5      6
A:   2.00   1.00   0.00   1.00   0.00   0.00   2.00
C:   1.00   3.00   0.00   2.00   4.00   0.00   1.00
G:   0.00   0.00   0.00   0.00   0.00   0.00   0.00
T:   1.00   0.00   4.00   0.00   0.00   4.00   0.00

>>> print(counts["T"][5])
4.0

Information Content

A potentially useful measure of evolutionary conservation is the information content of a sequence.

A useful introduction to information theory targeted towards molecular biologists can be found at http://www.lecb.ncifcrf.gov/~toms/paper/primer/. For our purposes, we will be looking at the information content of a consensus sequence, or a portion of a consensus sequence. We calculate information content at a particular column in a multiple sequence alignment using the following formula:

\[IC_{j} = \sum_{i=1}^{N_{a}} P_{ij} \mathrm{log}\left(\frac{P_{ij}}{Q_{i}}\right)\]

where:

• \(IC_{j}\) – The information content for the \(j\)-th column in an alignment.

• \(N_{a}\) – The number of letters in the alphabet.

• \(P_{ij}\) – The frequency of a particular letter \(i\) in the \(j\)-th column (i. e. if G occurred 3 out of 6 times in an alignment column, this would be 0.5)

• \(Q_{i}\) – The expected frequency of a letter \(i\). This is an optional argument, usage of which is left at the user’s discretion. By default, it is automatically assigned to \(0.05 = 1/20\) for a protein alphabet, and \(0.25 = 1/4\) for a nucleic acid alphabet. This is for getting the information content without any assumption of prior distributions. When assuming priors, or when using a non-standard alphabet, you should supply the values for \(Q_{i}\).

Well, now that we have an idea what information content is being calculated in Biopython, let’s look at how to get it for a particular region of the alignment.

First, we need to use our alignment to get an alignment summary object, which we’ll assume is called summary_align (see section Calculating summary information) for instructions on how to get this. Once we’ve got this object, calculating the information content for a region is as easy as:

>>> e_freq_table = {"A": 0.3, "G": 0.2, "T": 0.3, "C": 0.2}
>>> info_content = summary_align.information_content(
...     2, 6, e_freq_table=e_freq_table, chars_to_ignore=["N"]
... )
>>> info_content  
6.3910647...

Now, info_content will contain the relative information content over the region [2:6] in relation to the expected frequencies.

The value return is calculated using base 2 as the logarithm base in the formula above. You can modify this by passing the parameter log_base as the base you want:

>>> info_content = summary_align.information_content(
...     2, 6, e_freq_table=e_freq_table, log_base=10, chars_to_ignore=["N"]
... )
>>> info_content  
1.923902...

By default nucleotide or amino acid residues with a frequency of 0 in a column are not take into account when the relative information column for that column is computed. If this is not the desired result, you can use pseudo_count instead.

>>> info_content = summary_align.information_content(
...     2, 6, e_freq_table=e_freq_table, chars_to_ignore=["N", "-"], pseudo_count=1
... )
>>> info_content  
4.299651...

In this case, the observed frequency \(P_{ij}\) of a particular letter \(i\) in the \(j\)-th column is computed as follows:

\[P_{ij} = \frac{n_{ij} + k\times Q_{i}}{N_{j} + k}\]

where:

• \(k\) – the pseudo count you pass as argument.

• \(k\) – the pseudo count you pass as argument.

• \(Q_{i}\) – The expected frequency of the letter \(i\) as described above.

Well, now you are ready to calculate information content. If you want to try applying this to some real life problems, it would probably be best to dig into the literature on information content to get an idea of how it is used. Hopefully your digging won’t reveal any mistakes made in coding this function!

Getting a new-style Alignment object

Use the alignment property to create a new-style Alignment object (see section Alignment objects) from an old-style MultipleSeqAlignment object:

>>> type(msa)
<class 'Bio.Align.MultipleSeqAlignment'>
>>> print(msa)
Alignment with 4 rows and 7 columns
ACTCCTA seq1
AAT-CTA seq2
CCTACT- seq3
TCTCCTC seq4
>>> alignment = msa.alignment
>>> type(alignment)
<class 'Bio.Align.Alignment'>
>>> print(alignment)
seq1              0 ACTCCTA 7
seq2              0 AAT-CTA 6
seq3              0 CCTACT- 6
seq4              0 TCTCCTC 7

Note that the alignment property creates and returns a new Alignment object that is consistent with the information stored in the MultipleSeqAlignment object at the time the Alignment object is created. Any changes to the MultipleSeqAlignment after calling the alignment property will not propagate to the Alignment object. However, you can of course call the alignment property again to create a new Alignment object consistent with the updated MultipleSeqAlignment object.

Calculating a substitution matrix from a multiple sequence alignment

You can create your own substitution matrix from an alignment. In this example, we’ll first read a protein sequence alignment from the Clustalw file protein.aln (also available online here)

>>> from Bio import AlignIO
>>> filename = "protein.aln"
>>> msa = AlignIO.read(filename, "clustal")

Section ClustalW contains more information on doing this.

The substitutions property of the alignment stores the number of times different residues substitute for each other:

>>> observed_frequencies = msa.substitutions

To make the example more readable, we’ll select only amino acids with polar charged side chains:

>>> observed_frequencies = observed_frequencies.select("DEHKR")
>>> print(observed_frequencies)
       D      E      H      K      R
D 2360.0  255.5    7.5    0.5   25.0
E  255.5 3305.0   16.5   27.0    2.0
H    7.5   16.5 1235.0   16.0    8.5
K    0.5   27.0   16.0 3218.0  116.5
R   25.0    2.0    8.5  116.5 2079.0

Rows and columns for other amino acids were removed from the matrix.

Next, we normalize the matrix:

>>> import numpy as np
>>> observed_frequencies /= np.sum(observed_frequencies)

Summing over rows or columns gives the relative frequency of occurrence of each residue:

>>> residue_frequencies = np.sum(observed_frequencies, 0)
>>> print(residue_frequencies.format("%.4f"))
D 0.2015
E 0.2743
H 0.0976
K 0.2569
R 0.1697

>>> sum(residue_frequencies) == 1.0
True

The expected frequency of residue pairs is then

>>> expected_frequencies = np.dot(
...     residue_frequencies[:, None], residue_frequencies[None, :]
... )
>>> print(expected_frequencies.format("%.4f"))
       D      E      H      K      R
D 0.0406 0.0553 0.0197 0.0518 0.0342
E 0.0553 0.0752 0.0268 0.0705 0.0465
H 0.0197 0.0268 0.0095 0.0251 0.0166
K 0.0518 0.0705 0.0251 0.0660 0.0436
R 0.0342 0.0465 0.0166 0.0436 0.0288

Here, residue_frequencies[:, None] creates a 2D array consisting of a single column with the values of residue_frequencies, and residue_frequencies[None, :] a 2D array with these values as a single row. Taking their dot product (inner product) creates a matrix of expected frequencies where each entry consists of two residue_frequencies values multiplied with each other. For example, expected_frequencies['D', 'E'] is equal to residue_frequencies['D'] * residue_frequencies['E'].

We can now calculate the log-odds matrix by dividing the observed frequencies by the expected frequencies and taking the logarithm:

>>> m = np.log2(observed_frequencies / expected_frequencies)
>>> print(m)
      D    E    H     K    R
D   2.1 -1.5 -5.1 -10.4 -4.2
E  -1.5  1.7 -4.4  -5.1 -8.3
H  -5.1 -4.4  3.3  -4.4 -4.7
K -10.4 -5.1 -4.4   1.9 -2.3
R  -4.2 -8.3 -4.7  -2.3  2.5

This matrix can be used as the substitution matrix when performing alignments. For example,

>>> from Bio.Align import PairwiseAligner
>>> aligner = PairwiseAligner()
>>> aligner.substitution_matrix = m
>>> aligner.gap_score = -3.0
>>> alignments = aligner.align("DEHEK", "DHHKK")
>>> print(alignments[0])
target            0 DEHEK 5
                  0 |.|.| 5
query             0 DHHKK 5

>>> print("%.2f" % alignments.score)
-2.18
>>> score = m["D", "D"] + m["E", "H"] + m["H", "H"] + m["E", "K"] + m["K", "K"]
>>> print("%.2f" % score)
-2.18

Alignment Tools

There are lots of algorithms out there for aligning sequences, both pairwise alignments and multiple sequence alignments. These calculations are relatively slow, and you generally wouldn’t want to write such an algorithm in Python. For pairwise alignments, you can use Biopython’s PairwiseAligner (see Chapter Pairwise sequence alignment), which is implemented in C and therefore fast. Alternatively, you can run an external alignment program by invoking it from Python. Normally you would:

1. Prepare an input file of your unaligned sequences, typically this will be a FASTA file which you might create using Bio.SeqIO (see Chapter Sequence Input/Output).

2. Run the alignment program by running its command using Python’s subprocess module.

3. Read the output from the tool, i.e. your aligned sequences, typically using Bio.AlignIO (see earlier in this chapter).

Here, we will show a few examples of this workflow.

ClustalW

ClustalW is a popular command line tool for multiple sequence alignment (there is also a graphical interface called ClustalX). Before trying to use ClustalW from within Python, you should first try running the ClustalW tool yourself by hand at the command line, to familiarize yourself the other options.

For the most basic usage, all you need is to have a FASTA input file, such as opuntia.fasta (available online or in the Doc/examples subdirectory of the Biopython source code). This is a small FASTA file containing seven prickly-pear DNA sequences (from the cactus family Opuntia). By default ClustalW will generate an alignment and guide tree file with names based on the input FASTA file, in this case opuntia.aln and opuntia.dnd, but you can override this or make it explicit:

>>> import subprocess
>>> cmd = "clustalw2 -infile=opuntia.fasta"
>>> results = subprocess.run(cmd, shell=True, stdout=subprocess.PIPE, text=True)

Notice here we have given the executable name as clustalw2, indicating we have version two installed, which has a different filename to version one (clustalw, the default). Fortunately both versions support the same set of arguments at the command line (and indeed, should be functionally identical).

You may find that even though you have ClustalW installed, the above command doesn’t work – you may get a message about “command not found” (especially on Windows). This indicated that the ClustalW executable is not on your PATH (an environment variable, a list of directories to be searched). You can either update your PATH setting to include the location of your copy of ClustalW tools (how you do this will depend on your OS), or simply type in the full path of the tool. Remember, in Python strings \n and \t are by default interpreted as a new line and a tab – which is why we’re put a letter “r” at the start for a raw string that isn’t translated in this way. This is generally good practice when specifying a Windows style file name.

>>> import os
>>> clustalw_exe = r"C:\Program Files\new clustal\clustalw2.exe"
>>> assert os.path.isfile(clustalw_exe), "Clustal W executable missing"
>>> cmd = clustalw_exe + " -infile=opuntia.fasta"
>>> results = subprocess.run(cmd, shell=True, stdout=subprocess.PIPE, text=True)

Now, at this point it helps to know about how command line tools “work”. When you run a tool at the command line, it will often print text output directly to screen. This text can be captured or redirected, via two “pipes”, called standard output (the normal results) and standard error (for error messages and debug messages). There is also standard input, which is any text fed into the tool. These names get shortened to stdin, stdout and stderr. When the tool finishes, it has a return code (an integer), which by convention is zero for success, while a non-zero return code indicates that an error has occurred.

In the example of ClustalW above, when run at the command line all the important output is written directly to the output files. Everything normally printed to screen while you wait is captured in results.stdout and results.stderr, while the return code is stored in results.returncode.

What we care about are the two output files, the alignment and the guide tree. We didn’t tell ClustalW what filenames to use, but it defaults to picking names based on the input file. In this case the output should be in the file opuntia.aln. You should be able to work out how to read in the alignment using Bio.AlignIO by now:

>>> from Bio import AlignIO
>>> align = AlignIO.read("opuntia.aln", "clustal")
>>> print(align)
Alignment with 7 rows and 906 columns
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273291|gb|AF191665.1|AF191

In case you are interested (and this is an aside from the main thrust of this chapter), the opuntia.dnd file ClustalW creates is just a standard Newick tree file, and Bio.Phylo can parse these:

>>> from Bio import Phylo
>>> tree = Phylo.read("opuntia.dnd", "newick")
>>> Phylo.draw_ascii(tree)
                             _______________ gi|6273291|gb|AF191665.1|AF191665
  __________________________|
 |                          |   ______ gi|6273290|gb|AF191664.1|AF191664
 |                          |__|
 |                             |_____ gi|6273289|gb|AF191663.1|AF191663
 |
_|_________________ gi|6273287|gb|AF191661.1|AF191661
 |
 |__________ gi|6273286|gb|AF191660.1|AF191660
 |
 |    __ gi|6273285|gb|AF191659.1|AF191659
 |___|
     | gi|6273284|gb|AF191658.1|AF191658

Chapter Phylogenetics with Bio.Phylo covers Biopython’s support for phylogenetic trees in more depth.

MUSCLE

MUSCLE is a more recent multiple sequence alignment tool than ClustalW. As before, we recommend you try using MUSCLE from the command line before trying to run it from Python.

For the most basic usage, all you need is to have a FASTA input file, such as opuntia.fasta (available online or in the Doc/examples subdirectory of the Biopython source code). You can then tell MUSCLE to read in this FASTA file, and write the alignment to an output file named opuntia.txt:

>>> import subprocess
>>> cmd = "muscle -align opuntia.fasta -output opuntia.txt"
>>> results = subprocess.run(cmd, shell=True, stdout=subprocess.PIPE, text=True)

MUSCLE will output the alignment as a FASTA file (using gapped sequences). The Bio.AlignIO module is able to read this alignment using format="fasta":

>>> from Bio import AlignIO
>>> align = AlignIO.read("opuntia.txt", "fasta")
>>> print(align)
Alignment with 7 rows and 906 columns
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273289|gb|AF191663.1|AF191663
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273291|gb|AF191665.1|AF191665
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273290|gb|AF191664.1|AF191664
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273287|gb|AF191661.1|AF191661
TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273286|gb|AF191660.1|AF191660
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273285|gb|AF191659.1|AF191659
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273284|gb|AF191658.1|AF191658

You can also set the other optional parameters; see MUSCLE’s built-in help for details.

EMBOSS needle and water

The EMBOSS suite includes the water and needle tools for Smith-Waterman algorithm local alignment, and Needleman-Wunsch global alignment. The tools share the same style interface, so switching between the two is trivial – we’ll just use needle here.

Suppose you want to do a global pairwise alignment between two sequences, prepared in FASTA format as follows:

>HBA_HUMAN
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP
AVHASLDKFLASVSTVLTSKYR

in a file alpha.faa, and secondly in a file beta.faa:

>HBB_HUMAN
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK
VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG
KEFTPPVQAAYQKVVAGVANALAHKYH

You can find copies of these example files with the Biopython source code under the Doc/examples/ directory.

The command to align these two sequences against each other using needle is as follows:

needle -outfile=needle.txt -asequence=alpha.faa -bsequence=beta.faa -gapopen=10 -gapextend=0.5

Why not try running this by hand at the command prompt? You should see it does a pairwise comparison and records the output in the file needle.txt (in the default EMBOSS alignment file format).

Even if you have EMBOSS installed, running this command may not work – you might get a message about “command not found” (especially on Windows). This probably means that the EMBOSS tools are not on your PATH environment variable. You can either update your PATH setting, or simply use the full path to the tool, for example:

C:\EMBOSS\needle.exe -outfile=needle.txt -asequence=alpha.faa -bsequence=beta.faa -gapopen=10 -gapextend=0.5

Next we want to use Python to run this command for us. As explained above, for full control, we recommend you use Python’s built-in subprocess module:

>>> import sys
>>> import subprocess
>>> cmd = "needle -outfile=needle.txt -asequence=alpha.faa -bsequence=beta.faa -gapopen=10 -gapextend=0.5"
>>> results = subprocess.run(
...     cmd,
...     stdout=subprocess.PIPE,
...     stderr=subprocess.PIPE,
...     text=True,
...     shell=(sys, platform != "win32"),
... )
>>> print(results.stdout)

>>> print(results.stderr)
Needleman-Wunsch global alignment of two sequences

Next we can load the output file with Bio.AlignIO as discussed earlier in this chapter, as the emboss format:

>>> from Bio import AlignIO
>>> align = AlignIO.read("needle.txt", "emboss")
>>> print(align)
Alignment with 2 rows and 149 columns
MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTY...KYR HBA_HUMAN
MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRF...KYH HBB_HUMAN

In this example, we told EMBOSS to write the output to a file, but you can tell it to write the output to stdout instead (useful if you don’t want a temporary output file to get rid of – use outfile=stdout argument):

>>> cmd = "needle -outfile=stdout -asequence=alpha.faa -bsequence=beta.faa -gapopen=10 -gapextend=0.5"
>>> child = subprocess.Popen(
...     cmd,
...     stdout=subprocess.PIPE,
...     stderr=subprocess.PIPE,
...     text=True,
...     shell=(sys.platform != "win32"),
... )
>>> align = AlignIO.read(child.stdout, "emboss")
>>> print(align)
Alignment with 2 rows and 149 columns
MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTY...KYR HBA_HUMAN
MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRF...KYH HBB_HUMAN

Similarly, it is possible to read one of the inputs from stdin (e.g. asequence="stdin").

This has only scratched the surface of what you can do with needle and water. One useful trick is that the second file can contain multiple sequences (say five), and then EMBOSS will do five pairwise alignments.