NAME

bioaln - Bio::Perl Alignment utility wrappers for use Bio::AlignIO, Bio::SimpleAlign and Bio::Align::Utilities

SYNOPSIS

bioaln options [alignment_file]

bioaln [-h | --help | --v | --version --man]

DESCRIPTION

bioaln performs common, routine manipulations of sequence alignments. By default, bioaln assumes that both the input and the output files are in CLUSTALW format so that multiple bioaln runs can be chained with UNIX pipes. Upper-case options are less commonly used.

OPTIONS

Alignment Descriptors

--avpid, -a

Calculate the average percent identity of an alignment. Returns the value alone.

Wraps Bio::SimpleAlign->average_percentage_identity().

--gapstate

bioaln --gapstate <alignment_file>

--length, -l

Print alignment length. Wraps Bio::SimpleAlign->length().

bioaln --length <alignment_file>

--listids, -L

List all sequence ids.

bioaln --listids <alignment_file>

--numseq, -n

Get number of sequences in alignment.

bioaln --numseq <alignment_file>

--window, -w

Calculate pairwise average sequence difference by windows (overlapping windows with fixed step of 1). Default value for window_size is 30.

bioaln --window window_size <alignment_file>

Alignment Viewers

--codon-view, -c

Print a CLUSTALW-like alignment, but separated by codons. Intended for use with DNA sequences. Block-final position numbers are printed at the end of every alignment block at the point of wrapping, and block-initial counts appear over first nucleotide in a block.

If invoked as --codon-view=n where n is some number, will print n codons per line. Other normally stackable options, such as --match, can be used alongside it. If piping through bioaln, ensure codon-view is used in the last invocation.

For bioaln -c input_DNA.aln when input_DNA.aln contains:

Seq1   ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAAATAAGC
Seq2   ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAAATAAGC
Seq3   ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAAATAAGT
Seq4   ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAAATAAGT
Seq5   ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAATAAGC
Seq6   ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAATAAGT
       ******** ** * *** *************** **** ********

you get:

                                                                     4
       1                                                             8
Seq1   ATG AAT AAA AAG ATA TAC AGC ATA GAA GAA TTA ATA GAT AAA ATA AGC
Seq2   ATG AAT AAT AAA ATA TAC AGC ATA GAA GAA TTA ATA GAT AAA ATA AGC
Seq3   ATG AAT AAA AAG ATA TAT AGC ATA GAA GAA TTA GTA GAT AAA ATA AGT
Seq4   ATG AAT AAA AAA ACA TAT AGC ATA GAA GAA TTA ATA GAT AAA ATA AGT
Seq5   ATG AAT AAA AAA ATA TAT AGC ATA GAA GAA TTA ATA GAC AAA ATA AGC
Seq6   ATG AAT AAA AAA ATA TAT AGC ATA GAA GAA TTA ATA GAC AAA ATA AGT

--match, -m

Go through all columns and change residues identical to the reference sequence to be the match character, '.' Wraps Bio::SimpleAlign->match().

bioaln --match <alignment_file>

With

For input:

Seq1           ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT
Seq2           ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACGATAAGC
Seq3           ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA--ATAAGC
Seq4           ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA--ATAAGT
Seq5           ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC
Seq6           ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA--ATAAGT
               ******** ** * *** *************** **** ***  *****

bioaln --match 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...........

Alignment filters which produce a new alignment

--consensus, -C

Add a consensus sequence to the end of the alignment with a certain threshold percent and id Consensus_<percent>. By default percent is 50. Wraps Bio::SimpleAlign->consensus_string().

bioaln --consensus 'percent' <alignment_file>

For bioaln --consensus '90' input.aln where input.aln contains:

Seq1                  MNNKIYSIEELIDKISMPVVAYAGEAKSFLREALEYAKNK
Seq2                  MNKKTYSIEELIDKISMPVVAYSGEAKSFLREALEHAKNK
Seq3                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq4                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq5                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq6                  MNKKIYSIEELVDKISMPVVAYSGEAKSFLREALEYAKNK
                      **:* ******:**********:************:****

you get

Seq1                  MNNKIYSIEELIDKISMPVVAYAGEAKSFLREALEYAKNK
Seq2                  MNKKTYSIEELIDKISMPVVAYSGEAKSFLREALEHAKNK
Seq3                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq4                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq5                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq6                  MNKKIYSIEELVDKISMPVVAYSGEAKSFLREALEYAKNK
Consensus_90          MN?K?YSIEEL?DKISMPVVAY?GEAKSFLREALE?AKNK
                      ** * ****** ********** ************ ****

--delete, -d

Delete sequences based on their id. Option takes a comma-separated list of ids.

bioaln --delete 'seq_id_1, seq_id_2, ... , seq_id_n' <alignment_file>

--dna2pep, -D

Turn a CDS alignment to a corresponding protein alignment. Wraps Bio::Align::Utilities->dna_to_aa_aln().

bioaln --dna2pep <cds_alignment>

--erasecol, -E

Remove columns with gap in designated sequence.

bioaln --erasecol 'seq_id' <alignment_file>

For bioaln --erasecol 'Seq5' input.aln where input.aln contains:

Seq1           ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT
Seq2           ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACGATAAGC
Seq3           ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA--ATAAGC
Seq4           ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA--ATAAGT
Seq5           ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC
Seq6           ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA--ATAAGT
               ******** ** * *** *************** **** ***  *****

you get output:

Seq1           ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA-ATAAGT
Seq2           ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACATAAGC
Seq3           ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA-ATAAGC
Seq4           ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA-ATAAGT
Seq5           ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAACATAAGC
Seq6           ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA-ATAAGT
               ******** ** * *** *************** **** *** *****

--input, -i

Input file format. See Bio::AlignIO for supported formats. By default, this is 'clustalw'. Wraps Bio::AlignIO->new().

bioaln --input 'format'

--nogaps, -g

Remove gaps (and returns an de-gapped alignment). Wraps Bio::SimpleAlign->remove_gaps().

bioaln --nogaps <alignment_file>

--output, -o

Output file format. see Bio::AlignIO for supported formats. By default, this is 'clustalw'. Wraps Bio::AlignIO->new().

bioaln --output 'format'

--pick, -p

Pick sequences based on their id. Option takes a comma-separated list of ids.

bioaln --pick 'seq_id_1, seq_id_2, ... , seq_id_n' <alignment_file>

--refseq, -r seqid

Change the reference sequence to be seq_id. Wraps Bio::SimpleAlign->set_new_reference().

bioaln --refseq 'seq_id' <alignment_file>

--slice, -s

Get a slice of the alignment. Wraps Bio::SimpleAlign->slice() with improvements.

Using a '-' character in the first or second position defaults to the beginning or end, respectively. Therefore specifying -s'-,-' is the same as grabbing the whole alignment.

bioaln --slice 'min,max' <alignment_file>

--slice'20,80' or --slice'20,80' or -s='20,80' or --slice='20,80' Slice from position 20 to 80, inclusive. --slice'-,80' Slice from beginning up to, and including position 80 --slice'20,-' Slice from position 20 up to, and including, the end of the alignment

NOTE: --slice'-,x' (where x is '-' or a position) does NOT work. Use --slice='-,x' instead.

--trimends

--varsites, -v

Extracts variable sites. Used in conjunction with -g: do not show sites with gaps in any sequence.

bioaln --varsites <alignment_file>

--uniq, -u.

Extract the alignment of unique sequences. Wraps Bio::SimpleAlign->uniq_seq().

bioaln --uniq <alignment_file>

For bioaln --uniq input.aln where input.aln contains:

seq1                  ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT
seq11                 ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT
seq2                  ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACGATAAGC
seq3                  ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA--ATAAGC
seq4                  ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA--ATAAGT
seq5                  ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC
seq7                  ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC
seq6                  ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA--ATAAGT
                      ******** ** * *** *************** **** ***  *****

you get:

seq1	ST1
seq11	ST1
seq2	ST2
seq3	ST3
seq4	ST4
seq5	ST5
seq7	ST5
seq6	ST6

ST1                   ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT
ST2                   ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACGATAAGC
ST3                   ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA--ATAAGC
ST4                   ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA--ATAAGT
ST5                   ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC
ST6                   ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA--ATAAGT
                      ******** ** * *** *************** **** ***  *****

--pep2dna, -P

Align CDS sequences according to their corresponding protein alignment. Wraps "/metacpan.org/pod/Bio::Align::Utilities#aa_to_dna_aln" in Bio::Align::Utilities->aa_to_dna_aln()https:.

bioaln --pep2dna 'unaligned_cds.fas' <protein_alignment>

--uppercase

Make an uppercase alignment.

bioaln --uppercase <alignment_file>

Evolutionary Analysis

--bootstrap, -b

Produced a bootstrapped alignment. Wraps Bio::Align::Utilities->bootstrap().

Note that only a single alignment is produced. To produce multiple bootstraped alignment, use BASH loop (see below)

Here is an example in bash:

# 10 bootstrapped alignments
for i in {1..10}; do
   bioaln --bootstrap foo.aln > foo.boot-$i.aln;
done

--conblocks, -B

Extract perfectly conserved blocks (PCBs, gap excluded) from an alignment, each to a new clustalw file. Default minimum length of PCB is 6 sites.

bioaln --conblocks <alignment_file>

With bioaln --conblocks input.aln where input.aln is:

Seq1           ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT
Seq2           ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACGATAAGC
Seq3           ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA--ATAAGC
Seq4           ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA--ATAAGT
Seq5           ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC
Seq6           ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA--ATAAGT
               ******** ** * *** *************** **** ***  *****

you get:

nuc.aln.slice-1.aln : file contents below. Site positions indicated after the '/'

Seq1/1-8              ATGAATAA
Seq2/1-8              ATGAATAA
Seq3/1-8              ATGAATAA
Seq4/1-8              ATGAATAA
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
                      ********

--concat, -A

Concatenate multiple alignments sharing the same set of unique IDs. This is normally used for concatenating individual gene alignments of the same set of samples to a single one for making a "supertree". Wraps Bio::Align::Utilities>cat().

bioaln --concat gene1.aln gene2.aln gene3.aln gene4.aln

or using wildcard to specify files:

bioaln --concat gene*.aln

--noflatname, -F

By default, sequence names do not contain 'begin-end'. This option turns ON 'begin-end' naming. Wraps Bio::SimpleAlign->set_displayname_flat().

bioaln --noflatname <alignment_file>

--aln-index, -I

Identify aligned position of a residue. Wraps Bio::SimpleAlign->column_from_residue_number().

bioaln --aln-index 'seq_id,position' <alignment_file>

--permute-states, -M

Generate an alignment with randomly permuted residues at each site. This operation removes phylogenetic signal among aligned sequences, if there is any in the original alignment. This is the basis of the Permutation Trail Prob (PTP) test of tree-ness of an alignment.

bioaln --permute-states <alignment_file>

--resample, -R

Picks n random sequences from input alignment and produces a new alignment consisting of those sequences.

If n is not given, default is the number of sequences in alignment divided by 2, rounded down.

This functionality uses an implementation of Reservoir Sampling, based on the algorithm found here: http://blogs.msdn.com/b/spt/archive/2008/02/05/reservoir-sampling.aspx

bioaln --resample 'n' <alignment_file>

For bioaln --resample 4 input.aln where input.aln contains

Seq1                  MNNKIYSIEELIDKISMPVVAYAGEAKSFLREALEYAKNK
Seq2                  MNKKTYSIEELIDKISMPVVAYSGEAKSFLREALEHAKNK
Seq3                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq4                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq5                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq6                  MNKKIYSIEELVDKISMPVVAYSGEAKSFLREALEYAKNK
                      **:* ******:**********:************:****

you get:

Seq2                  MNKKTYSIEELIDKISMPVVAYSGEAKSFLREALEHAKNK
Seq3                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq4                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq6                  MNKKIYSIEELVDKISMPVVAYSGEAKSFLREALEYAKNK
                      **** ******:***********************:****

--shuffle-sites, -S

Make a shuffled (not bootstraped) alignment. This operation randomizes alignment columns. It is used for testing the signficance of long-runs of conserved sites in an alignment (e.g., conserved intergenic spacers [IGSs]).

bioaln --shuffle-sites <alignment_file>

For bioaln --shuffle-sites input.aln

Seq1                  MNNKIYSIEELIDKISMPVVAYAGEAKSFLREALEYAKNK
Seq2                  MNKKTYSIEELIDKISMPVVAYSGEAKSFLREALEHAKNK
Seq3                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq4                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq5                  MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK
Seq6                  MNKKIYSIEELVDKISMPVVAYSGEAKSFLREALEYAKNK
                      **:* ******:**********:************:****

you get:

Seq1                  VIEELKYEKAAEAFIPNISEDASGKIRLKLMSVNAYKMYN
Seq2                  VIEELKYEKAAEAFIPNISEDASGKTRLKLMSVKSYKMHN
Seq3                  VIEELKYEKAAEAFIPNISEDASGKIRLKLMSVKSYKMYN
Seq4                  VIEELKYEKAAEAFIPNISEDASGKIRLKLMSVKSYKMYN
Seq5                  VIEELKYEKAAEAFIPNISEDASGKIRLKLMSVKSYKMYN
Seq6                  VIEELKYEKAAEAFVPNISEDASGKIRLKLMSVKSYKMYN
                      **************:********** *******::***:*

--select-third

Generate an alignment of every-third (mostly synonymous) bases (assuming a CDS alignment).

Common Options

--help, -h: Print a brief help message and exit.
--man: Print the manual page and exit.
--version, -V: Print current release version of this command and exit.

EXAMPLES

Alignment Descriptors

bioaln --avpid input.aln            # average percent identity
bioaln --gapstates  aln_file        # identify unique gaps (start, end, frequency, whether in bioaln --index 'B31,100' aln_file   # get aln column index of seq 'B31' residue 100
bioaln --length aln_file            # length of an alignment
bioaln --listids aln_file           # list all sequence IDs
bioaln --numseq aln_file            # number of aligned sequences
bioaln --window '30' aln_file       # average identifies for sliding [w]indows of 30
ternal)

Alignment Viewers

bioaln --codon-view aln_file             # codon view (groups of 3 nts)
bioaln --match input.aln                 # match view (show variable sites)

Alignment filters which produce a new alignment

bioaln --binary-informative
bioaln --consensus '90' aln_file         # add a 90% consensus sequence
bioaln --delete 'Seq1,Seq2' aln_input    # delete sequences
bioaln --dna2pep cds.aln                 # DNA alignment => protein alignment
bioaln --erasecol 'Seq5' input.aln       # erase sites gapped at Seq5
bioaln --input 'fasta' fasta_aln_file    # input is a FASTA alignment (CLUSTALW is dafault)
bioaln --nogaps aln_file                 # remove gapped sites
bioaln --output 'fasta' aln_file         # output a FASTA alignment (CLUSTALW is dafault)
bioaln --pep2dna 'cds.fas' pep.aln       # Back-align CDS seqs according to protein alignment
bioaln --pick 'Seq1, Seq2' aln_input     # pick sequences
bioaln --refseq 'seq_id' aln_file        # change reference (1st) sequence
bioaln --slice '10,20'                   # alignment slice from 10-20
bioaln --uniq aln_file                   # remove redundant sequences
bioaln --upperasealn_file                # turn into upper-case
bioaln --varsites aln_file               # show only variable sites

Evolutionary Analysis

bioaln --concat *.aln               # concattenate aln files
bioaln --conblocks aln_file         # extract conserved blocks
bioaln --shuffle-sitesaln_file      # shuffle sites (for testing conserved blocks)
bioaln --resample '10' aln_file     # [R]e-sampled an alignment of 10 sequences
bioaln --bootstrap aln_file         # bootstrap an alignment (for testing branch stability)
bioaln --permute-states aln_file    # permute at each site (for testing tree-ness)
bioaln --remove-third aln_file      # remove [T]hird site (assume coding sequences)

change alignment format

bioaln --input 'fasta' --output 'phylip'       # FASTA => PHYLIP
bioaln --input 'fasta' --output 'pmal'         # FASTA => PAML

Chaining with pipes

# Read a FASTA alignment, slice it, and calcualte percent identity:
bioaln -i'fasta' fasta.aln | bioaln -s'10,20' | bioaln -a

# Chaining with bioseq:
# Turn a coding-sequence alignment into a protein alignemnt (an alternative to C<--dna2pep>):

  bioaln --output fasta cds.aln | bioseq --translate 1 | bioaln --input fasta

CONTRIBUTORS

William McCaig <wmccaig at gmail dot com>
Girish Ramrattan <gramratt at gmail dot com>
Che Martin <che dot l dot martin at gmail dot com>
Yözen Hernández yzhernand at gmail dot com
Levy Vargas <levy dot vargas at gmail dot com>
Weigang Qiu (Maintainer)
Rocky Bernstein

To install Bio::BPWrapper, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::BPWrapper

CPAN shell

perl -MCPAN -e shell
install Bio::BPWrapper

For more information on module installation, please visit the detailed CPAN module installation guide.

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NAME

SYNOPSIS

DESCRIPTION

OPTIONS

Alignment Descriptors

Alignment Viewers

Alignment filters which produce a new alignment

Evolutionary Analysis

Common Options

EXAMPLES

Alignment Descriptors

Alignment Viewers

Alignment filters which produce a new alignment

Evolutionary Analysis

change alignment format

Chaining with pipes

SEE ALSO

CONTRIBUTORS

Module Install Instructions