Bio-BPWrapper
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Seq5/1-8 ATGAATAA
Seq6/1-8 ATGAATAA
********
nuc.aln.slice-19.aln:
Seq1/19-33 AGCATAGAAGAATTA
Seq2/19-33 AGCATAGAAGAATTA
Seq3/19-33 AGCATAGAAGAATTA
Seq4/19-33 AGCATAGAAGAATTA
Seq5/19-33 AGCATAGAAGAATTA
Seq6/19-33 AGCATAGAAGAATTA
***************
nuc.aln.slice-40.aln
Seq1/40-47 AAAATAAG
Seq2/40-47 AAAATAAG
Seq3/40-47 AAAATAAG
Seq4/40-47 AAAATAAG
Seq5/40-47 AAAATAAG
Seq6/40-47 AAAATAAG
********
=item --concat, -A
Concatenate multiple alignments sharing the same set of IDs. This is normally used for concatenating individual gene
alignments of the same set of samples to a single one for making a "supertree".
bioaln --concat gene1.aln gene2.aln gene3.aln gene4.aln
or using wildcard to specify multiple files (check with "ls *.aln" first to make sure of alignment order):
bioaln --concat gene*.aln
Two outputs:
1. concated alignment (in STANDOUT)
2. "concat.log" file, which shows mapped positions for a reference seq (specified by "-r" otherwise first sequence)
=item --consensus, -C 'percent' (default 50)
Add a consensus sequence to the end of the alignment with a certain threshold percent and id Consensus_<percent>.
=item --delete, -d 'seq_id1,seq_id2,etc'
Delete sequences based on their ids. Option takes a comma-separated list of ids.
=item --dna2pep, -D
Turn an in-frame protein-coding sequence alignment to a corresponding protein alignment.
=item --gap-char '.'
Change '.' (e.g., from BCFtools, which causes problem for --uniq-seq) to default gap character '-'
=item --gap-states
Prints one alignment gap per line, including its start, end, whether in-frame, whether on-edge, how many copies, and alignment length. (Can't remember what context this was developed at first; ignore)
=item --gap-states2
Prints one alignment gap per column, including its start-end as column heading and presence/absence (1/0) in each sequence.
=item --input, -i 'format'
Now it tries to guess the format. BLAST outputs still need to be specified
[Deprecated except for blast output] Specify input file format. Common ones include 'clustalw' (default), 'fasta' and 'phylip'. See L<Bio::AlignIO> for supported formats.
In addition, it reads NCBI-blast outputs as well. e.g., bioaln -i'blast' blast.out.
=item --length, -l
Print alignment length.
=item --listids, -L
List all sequence ids.
=item --match, -m
Go through all columns and change residues identical to the reference sequence to be the match character, '.'.
For input:
Seq1 ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT
Seq2 ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACGATAAGC
Seq3 ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA--ATAAGC
Seq4 ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA--ATAAGT
Seq5 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC
Seq6 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA--ATAAGT
******** ** * *** *************** **** *** *****
C<bioaln -m input.aln> gives:
Seq1 ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT
Seq2 .................C...............A........CG.....C
Seq3 ........T..A.....C...............A...............C
Seq4 ...........A.C...................A................
Seq5 ...........A.....................A....C...C......C
Seq6 ...........A.....................A....C...........
=item --no-flat, -F
By default, sequence names do not contain 'begin-end'. This option turns ON 'begin-end' naming.
=item --no-gaps, -g
Remove gaps (and returns an de-gapped alignment).
=item --num-seq, -n
Print number of sequences in alignment.
=item --output, -o 'format'
Output file format. Common ones include 'clustalw' (default), 'fasta' and 'phylip'. See L<Bio::AlignIO> for supported formats. An additional format 'paml' is supported.
=item --pair-diff
Print pairwise sequence differences, including columns: seqA, seqB, num_variable_sites (no gap), num_pair_diff (no gap), total_pair_length (no gap), percent identity, fraction diff, and pair_diff/num_variable. For DNA seqs, it counts any non-ATCG's (...
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