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Easy Manipulation of Multiple Sequence Alignments (Concatenation and Format Conversion)
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kyungtaekLIM/seqlim
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Concatenate and Convert Multiple Sequence Alignments
seqlim includes a python library and an executable for manipulating biological sequences. It concatenates multiple sequence alignments (MSAs) horizontally or vertically, and converts MSAs into various formats (fasta, phylip, nexus, msf, tsv, and csv). The horizontal concatenation of MSAs is often used for multi-loci/multi-gene phylogenetic analysis and phylogenomics.
- Install Python 2.7 or higher, Python installers are available athttps://www.python.org/.
- Clone or download this repo and install using setup.py.
$ python setup.py install- Confirm the installation of
seqlimexecutable.
$ seqlim -h- Confirm the installation of
seqlimlibrary.
$ python>>> from seqlim import MSeq- Suppose two sequence files in FASTA format in
./test/fasta.
`Locus1.fasta` >Escheri1 CCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC >Enteroc1 UGUGGUGGCGAUAGCGAGAAGGAUACACCUGUUCCCAUGCCGAACACAGAAGUUAAGC`Locus2.fasta` >Escheri2 UAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACU--GCCAGGC >Enteroc2 UAGCGCCGAUUGUAGUGAAGGGUUUCCCUUUGUGAGAGUAGG--ACGUCGCCACGC- Concatenate these files horizontally.
$ seqlim cath ./test/fasta>Escheri1CCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACU--GCCAGGC>Enteroc1UGUGGUGGCGAUAGCGAGAAGGAUACACCUGUUCCCAUGCCGAACACAGAAGUUAAGCUAGCGCCGAUUGUAGUGAAGGGUUUCCCUUUGUGAGAGUAGG--ACGUCGCCACGC- Concatenate the files vertically.
$ seqlim catv ./test/fasta>Escheri1CCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC>Enteroc1UGUGGUGGCGAUAGCGAGAAGGAUACACCUGUUCCCAUGCCGAACACAGAAGUUAAGC>Escheri2UAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACU--GCCAGGC>Enteroc2UAGCGCCGAUUGUAGUGAAGGGUUUCCCUUUGUGAGAGUAGG--ACGUCGCCACGC- Set an input sequence format after
-infmt.seqlimaccepts 'fasta', 'fas', 'mfa', 'fna', 'fsa' or 'fa' for FASTA format, 'phylip' or 'phy' for PHYLIP format and 'msf' for MSF format.
$ seqlim -infmt phylip cath ./test/phylip>Escheri1CCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC>Enteroc1UGUGGUGGCGAUAGCGAGAAGGAUACACCUGUUCCCAUGCCGAACACAGAAGUUAAGC>Escheri2UAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACU--GCCAGGC>Enteroc2UAGCGCCGAUUGUAGUGAAGGGUUUCCCUUUGUGAGAGUAGG--ACGUCGCCACGC- Set an output sequence format after
-outfmt.seqlimaccepts 'fasta', 'fas', 'mfa', 'fna', 'fsa' or 'fa' for FASTA format, 'phylip' or 'phy' for PHYLIP format, 'nexus', 'nex' or 'nxs' for NEXUS format, 'msf' for MSF format, 'csv' for CSV format and 'tsv' for TSV format.
$ seqlim -outfmt phylip cath ./test/fasta 2 114Escheri1 CCUGGCGGCC GUAGCGCGGU GGUCCCACCU GACCCCAUGC CGAACUCAGA AGUGAAACUAEnteroc1 UGUGGUGGCG AUAGCGAGAA GGAUACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUA GCGCCGAUGG UAGUGUGGGG UCUCCCCAUG CGAGAGUAGG GAACU--GCC AGGC GCGCCGAUUG UAGUGAAGGG UUUCCCUUUG UGAGAGUAGG --ACGUCGCC ACGC- The line and block lengths of sequences can be adjusted using
-line_lengthand-block_length, respectively.
$ seqlim -outfmt phylip -line_length 50 -block_length 5 cath ./test/fasta 2 114Escheri1 CCUGG CGGCC GUAGC GCGGU GGUCC CACCU GACCC CAUGC CGAAC UCAGAEnteroc1 UGUGG UGGCG AUAGC GAGAA GGAUA CACCU GUUCC CAUGC CGAAC ACAGA AGUGA AACUA GCGCC GAUGG UAGUG UGGGG UCUCC CCAUG CGAGA GUAGG AGUUA AGCUA GCGCC GAUUG UAGUG AAGGG UUUCC CUUUG UGAGA GUAGG GAACU --GCC AGGC --ACG UCGCC ACGC- Save an output.
$ seqlim -o ./test/temp/concatenated.fasta cath ./test/fasta- Just format conversion.
$ seqlim -outfmt phylip -o ./test/temp/converted.phylip cnvt ./test/fasta/locus1.fasta- Convert all sequence files in
./test/fastato another format (phylip) and save them in./test/phylip.
$ seqlim -o ./test/phylip -outfmt phylip cnvt ./test/fasta