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Goalign: toolkit and api for alignment manipulation

Commands

unalign

Unaligns an input alignment, by removing indels.

The output is in Fasta format, whatever the input format is (Fasta or Phylip).

Output sequences are free from all indel charachers "-".

As there may be several alignments in the input alignment (phylip format), output files are prefixed with argument given to "--output-prefix", and suffixed with an index and the extension ".fa".

If --output-prefix is set to "-" or "stdout", all sequences are printed on stdout

Example:

goalign unalign -i align.ph -p -o seq_

If align contains 3 alignments, this will generate 3 files:

  • seq_000001.fa
  • seq_000002.fa
  • seq_000003.fa

Usage

Usage:
  goalign unalign [flags]

Flags:
  -o, --output-prefix string   Unaligned alignment output file prefix (default "stdout")

Global Flags:
  -i, --align string   Alignment input file (default "stdin")
  -p, --phylip         Alignment is in phylip? False=Fasta
  -t, --threads int    Number of threads (default 1)
  --input-strict       Strict phylip input format (only used with -p)

Examples

  • Generating random alignment, adding 50% gaps in 50% of the sequences, and unaligning it:
# Gapped alignment
goalign random --seed 10 -p | goalign mutate gaps --seed 10 -p -n 0.5 -r 0.5
# Gapped alignment => unaligned
goalign random --seed 10 -p | goalign mutate gaps --seed 10 -p -n 0.5 -r 0.5 | goalign unalign -p

Should output:

  10   100
Seq0000  GATTAATTTG CCGTAGGCCA GAATCTGAAG ATCGAACACT TTAAGTTTTC ACTTCTAATG
Seq0001  --TC------ AA---TTG-- TA-AA-GG-G -ATT-CA--G ------A-G- CT-T-T-T-C
Seq0002  -T-----CGG GC--A-T--T G---GA-CAA GGTT-A---- -----A--GC --CATGATC-
Seq0003  GAGTGGAGGC TTTATGGCAC AAGGTATTAG AGACTGAGGG GCACCCCGGC ATGGTAAGCA
Seq0004  -AT-GC---- -AT--C--G- -C-GT--C-- GG-AA-G--T AC--T-CAC- A---A-AC-C
Seq0005  AGTTTGACTA TGAGCGCCGG CTTAGTGCTG ACAGTGATGC TCCGTTGTAA GGGTCCTGAT
Seq0006  T--C-A---- G-G--A-GT- CGT--T-G-A --AA-CAGCG -----C-CC- ACA------C
Seq0007  CTGGTAATAC CTGCGCTATT TCGTCAGTTC GTGTACGGGT AACGATAGCG GTTAATGCTT
Seq0008  T-G-T--CCC AC--T--C-A CCT------- -G--ATC-G- T-C-C----T GG----CTT-
Seq0009  ACCTACGGCT CTAGACAGCT GAAGTCCGGT TCCGAGCACT GTACGGAAAC TTGAAAAGGC

   GAGAGGACTA GTTCATACTT TTTAAACACT TTTACATCGA
   GG-TGAA--A C----G---T GT-AA---TA -G---ATGTG
   C-C--GG-C- -T--G---GA AG-----A-A -ATGA-CCC-
   GGAGCCATCG CGAAGGCTTC AGGTATCTTC CTGTGTTACC
   CG--GCTA-- CG-CTC---- T-CTT-T-T- C----TCT--
   GTTCTTGTGC TCGCGCATAT TAGAGCTGAG TTTCCCAAAG
   T--GT-GCTC CT--C--C-A ---G-GG-CC TG-G-T--C-
   ATTCCGATCA GCTCACACCC ATGAAGGTGG CTCTGGAGCC
   -T----T-GG -CCCCAGG-- TCA--C--GT -A-CTCT---
   TCGACGGAGG CTTGTTCCGC AGAGTGGGAC TATAACATAC

Then:

>Seq0000
GATTAATTTGCCGTAGGCCAGAATCTGAAGATCGAACACTTTAAGTTTTCACTTCTAATGGAGAGGACTAGTTCATACTT
TTTAAACACTTTTACATCGA
>Seq0001
TCAATTGTAAAGGGATTCAGAGCTTTTCGGTGAAACGTGTAATAGATGTG
>Seq0002
TCGGGCATTGGACAAGGTTAAGCCATGATCCCGGCTGGAAGAAATGACCC
>Seq0003
GAGTGGAGGCTTTATGGCACAAGGTATTAGAGACTGAGGGGCACCCCGGCATGGTAAGCAGGAGCCATCGCGAAGGCTTC
AGGTATCTTCCTGTGTTACC
>Seq0004
ATGCATCGCGTCGGAAGTACTCACAAACCCGGCTACGCTCTCTTTTCTCT
>Seq0005
AGTTTGACTATGAGCGCCGGCTTAGTGCTGACAGTGATGCTCCGTTGTAAGGGTCCTGATGTTCTTGTGCTCGCGCATAT
TAGAGCTGAGTTTCCCAAAG
>Seq0006
TCAGGAGTCGTTGAAACAGCGCCCACACTGTGCTCCTCCAGGGCCTGGTC
>Seq0007
CTGGTAATACCTGCGCTATTTCGTCAGTTCGTGTACGGGTAACGATAGCGGTTAATGCTTATTCCGATCAGCTCACACCC
ATGAAGGTGGCTCTGGAGCC
>Seq0008
TGTCCCACTCACCTGATCGTCCTGGCTTTTGGCCCCAGGTCACGTACTCT
>Seq0009
ACCTACGGCTCTAGACAGCTGAAGTCCGGTTCCGAGCACTGTACGGAAACTTGAAAAGGCTCGACGGAGGCTTGTTCCGC
AGAGTGGGACTATAACATAC