# Alignment descriptors: bioaln -l aln_file # [l]ength of an alignment bioaln -n aln_file # [n]umber of aligned sequences bioaln -L aln_file # [L]ist all sequence IDs bioaln -a input.aln # [a]verage percent identity bioaln -w '30' aln_file # average identifies for sliding [w]indows of 30 bioaln -I 'B31,100' aln_file # get aln column [I]ndex of seq 'B31' residue 100 bioaln --gapstates aln_file # identify unique gaps (start, end, frequency, whether internal) # Alignment viewers: bioaln -m input.aln # [m]atch view (show variable sites) bioaln -c aln_file # [c]odon view (groups of 3 nts) # Alignment filters (produce a new alignment): bioaln -i 'fasta' fasta_aln_file # [i]nput is a FASTA alignment (CLUSTALW is dafault) bioaln -o 'fasta' aln_file # [o]utput a FASTA alignment (CLUSTALW is dafault) bioaln -g aln_file # remove [g]apped sites bioaln -s '10,20' # alignment [s]lice from 10-20 bioaln -r 'seq_id' aln_file # change [r]eference (1st) sequence bioaln -d 'Seq1,Seq2' aln_input # [d]elete sequences bioaln -p 'Seq1, Seq2' aln_input # [p]ick sequences bioaln -u aln_file # [u]nique-fy sequences (remove redundant seqs) bioaln -v aln_file # show only variable sites bioaln -C '90' aln_file # add a 90% [C]onsensus sequence bioaln -D cds.aln # D(na) alignment => protein alignment bioaln -E 'Seq5' input.aln # [E]rase sites gapped at Seq5 bioaln -P 'cds.fas' pep.aln # Back-align CDS seqs according to [P]rotein alignment bioaln -U aln_file # turn into [U]pper-case # Evolutionary analysis: bioaln -A *.aln # conc(A)tenate aln files bioaln -B aln_file # extract conserved [B]locks bioaln -S aln_file # [S]huffle sites (for testing conserved blocks) bioaln -R '10' aln_file # [R]e-sampled an alignment of 10 sequences bioaln -b aln_file # [b]ootstrap an alignment (for testing branch stability) bioaln -M aln_file # per[m]ute at each site (for testing tree-ness) bioaln -T aln_file # extract [T]hird site (assume coding sequences) bioaln --remove-third aln_file # remove [T]hird site (assume coding sequences) # change alignment format: bioaln -i 'fasta' -o 'phylip' # FASTA => PHYLIP bioaln -i 'fasta' -o '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 -D): bioaln -o'fasta' cds.aln | bioseq -t1 | bioaln -i'fasta'
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.
Print a brief help message and exit.
Calculate the average percent identity of an alignment. Returns the value alone. Wrap Bio::SimpleAlign->average_percentage_identity().
Usage: bioaln -a <alignment_file>
Produced a bootstrapped alignment. Wrap Bio::Align::Utilities->bootstrap(). Note that only a single alignment is produced. To produce multiple bootstraped alignment, use BASH loop (see below)
Usage: bioaln -b <alignment_file> (single bootstrapped alignment) Usage: for i in {1..10}; do bioaln -b foo.aln > foo.boot-$i.aln; done (10 bootstrapped alignments)
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 -m, can be used alongside it. If piping through bioaln, ensure codon-view is used in the last invocation.
Usage: bioaln -c <alignment_file>
EXAMPLE: bioaln -c input_DNA.aln
INPUT:
Seq1 ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAAATAAGC Seq2 ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAAATAAGC Seq3 ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAAATAAGT Seq4 ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAAATAAGT Seq5 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAATAAGC Seq6 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAATAAGT ******** ** * *** *************** **** ********
OUTPUT: 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
Delete sequences based on their id. Option takes a comma-separated list of ids.
Usage: bioaln -d 'seq_id_1, seq_id_2, ... , seq_id_n' <alignment_file>
Remove gaps (and returns an de-gapped alignment). Wrap Bio::SimpleAlign->remove_gaps();
Usage: bioaln -g <alignment_file>
Input file format (see Bio::AlignIO for supported formats). By default, this is 'clustalw'. Wrap Bio::AlignIO->new().
Usage: bioaln -i 'format'
Print alignment length. Wrap Bio::SimpleAlign->length().
Usage: bioaln -l <alignment_file>
Go through all columns and change residues identical to the reference sequence to be the match character, '.' Wrap Bio::SimpleAlign->match().
Usage: bioaln -m <alignment_file>
EXAMPLE: bioaln -m input.aln
Seq1 ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT Seq2 ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACGATAAGC Seq3 ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA--ATAAGC Seq4 ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA--ATAAGT Seq5 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC Seq6 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA--ATAAGT ******** ** * *** *************** **** *** *****
OUTPUT:
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...........
Get number of sequences in alignment.
Usage: bioaln -n <alignment_file>
Output file format (see Bio::AlignIO for supported formats). By default, this is 'clustalw'. Wrap Bio::AlignIO->new().
Usage: bioaln -o 'format'
Pick sequences based on their id. Option takes a comma-separated list of ids.
Usage: bioaln -p 'seq_id_1, seq_id_2, ... , seq_id_n' <alignment_file>
Change the reference sequence to be seq_id. Wrap Bio::SimpleAlign->set_new_reference().
Usage: bioaln -r 'seq_id' <alignment_file>
Get a slice of the alignment. Wrap 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.
Usage: bioaln -s 'min,max' <alignment_file>
-s'20,80' or --slice'20,80' or -s='20,80' or --slice='20,80' Slice from position 20 to 80, inclusive. -s'-,80' Slice from beginning up to, and including position 80 -s'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.
Extract the alignment of unique sequences. Wrap Bio::SimpleAlign->uniq_seq().
Usage: bioaln -u <alignment_file>
EXAMPLE: bioaln -u input.aln
seq1 ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT seq11 ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA--ATAAGT seq2 ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACGATAAGC seq3 ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA--ATAAGC seq4 ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA--ATAAGT seq5 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC seq7 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAAC-ATAAGC seq6 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA--ATAAGT ******** ** * *** *************** **** *** *****
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 ******** ** * *** *************** **** *** *****
Extracts variable sites. Used in conjunction with -g: do not show sites with gaps in any sequence.
Usage: bioaln -v <alignment_file>
Calculate pairwise average sequence difference by windows (overlapping windows with fixed step of 1). Default value for window_size is 30.
Usage: bioaln -w 'window_size'[default is 30] <alignment_file>
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". Wrap Bio::Align::Utilities->cat().
Usage: bioaln -A gene1.aln gene2.aln gene3.aln gene4.aln,
Or: using wildcard to specify files:
Usage: bioaln -A gene*.aln
Extract perfectly conserved blocks (PCBs, gap excluded) from an alignment, each to a new clustalw file. Default minimum length of PCB is 6 sites.
Usage: bioaln -B <alignment_file>
EXAMPLE: bioaln -B input.aln
OUTPUT: files containing perfectly conserved blocks
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 ********
Add a consensus sequence to the end of the alignment with a certain threshold percent and id Consensus_<percent>. By default percent is 50. Wrap Bio::SimpleAlign->consensus_string().
Usage: bioaln -C 'percent' <alignment_file>
EXAMPLE: bioaln -C '90' input.aln
Seq1 MNNKIYSIEELIDKISMPVVAYAGEAKSFLREALEYAKNK Seq2 MNKKTYSIEELIDKISMPVVAYSGEAKSFLREALEHAKNK Seq3 MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK Seq4 MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK Seq5 MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK Seq6 MNKKIYSIEELVDKISMPVVAYSGEAKSFLREALEYAKNK **:* ******:**********:************:****
Seq1 MNNKIYSIEELIDKISMPVVAYAGEAKSFLREALEYAKNK Seq2 MNKKTYSIEELIDKISMPVVAYSGEAKSFLREALEHAKNK Seq3 MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK Seq4 MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK Seq5 MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK Seq6 MNKKIYSIEELVDKISMPVVAYSGEAKSFLREALEYAKNK Consensus_90 MN?K?YSIEEL?DKISMPVVAY?GEAKSFLREALE?AKNK ** * ****** ********** ************ ****
Turn a CDS alignment to a corresponding protein alignment. Wrap Bio::Align::Utilities->dna_to_aa_aln().
Usage: bioaln -D <cds_alignment>
Remove columns with gap in designated sequence.
Usage: bioaln -E 'seq_id' <alignment_file>
EXAMPLE: bioaln -E 'Seq5' input.aln
Seq1 ATGAATAAAAAGATATATAGCATAGAAGAATTAGTAGATAAA-ATAAGT Seq2 ATGAATAAAAAGATATACAGCATAGAAGAATTAATAGATAAACATAAGC Seq3 ATGAATAATAAAATATACAGCATAGAAGAATTAATAGATAAA-ATAAGC Seq4 ATGAATAAAAAAACATATAGCATAGAAGAATTAATAGATAAA-ATAAGT Seq5 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAACATAAGC Seq6 ATGAATAAAAAAATATATAGCATAGAAGAATTAATAGACAAA-ATAAGT ******** ** * *** *************** **** *** *****
By default, sequence names do not contain 'begin-end'. This option turns ON 'begin-end' naming. Wrap Bio::SimpleAlign->set_displayname_flat().
Usage: bioaln -F <alignment_file>
Identify aligned position of a residue. Wrap Bio::SimpleAlign->column_from_residue_number().
Usage: bioaln -I 'seq_id,position' <alignment_file>
List all sequence ids.
Usage: bioaln -L <alignment_file>
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.
Usage: bioaln -M <alignment_file>
Align CDS sequences according to their corresponding protein alignment. Wrap Bio::Align::Utilities->aa_to_dna_aln().
Usage: bioaln -P 'unaligned_cds.fas' <protein_alignment>
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
Usage: bioaln -R 'n' <alignment_file>
EXAMPLE: bioaln -R4 input.aln
Seq2 MNKKTYSIEELIDKISMPVVAYSGEAKSFLREALEHAKNK Seq3 MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK Seq4 MNKKIYSIEELIDKISMPVVAYSGEAKSFLREALEYAKNK Seq6 MNKKIYSIEELVDKISMPVVAYSGEAKSFLREALEYAKNK **** ******:***********************:****
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]).
Usage: bioaln -S <alignment_file>
EXAMPLE: bioaln -S input.aln
Seq1 VIEELKYEKAAEAFIPNISEDASGKIRLKLMSVNAYKMYN Seq2 VIEELKYEKAAEAFIPNISEDASGKTRLKLMSVKSYKMHN Seq3 VIEELKYEKAAEAFIPNISEDASGKIRLKLMSVKSYKMYN Seq4 VIEELKYEKAAEAFIPNISEDASGKIRLKLMSVKSYKMYN Seq5 VIEELKYEKAAEAFIPNISEDASGKIRLKLMSVKSYKMYN Seq6 VIEELKYEKAAEAFVPNISEDASGKIRLKLMSVKSYKMYN **************:********** *******::***:*
Generate an alignment of every-third (mostly synonymous) bases (assuming a CDS alignment).
Usage: bioaln -T <alignment_file>
Make an uppercase alignment.
Usage: bioaln -U <alignment_file>
Print current release version of bp-utils.
Usage: bioseq -V
Perl 5.10 or greater, BioPerl
Please see project wiki page https://github.com/bioperl/bp-utils/wiki for documentation and use cases.
Please email weigang@genectr.hunter.cuny.edu.
William McCaig <wmccaig at gmail dot com> Che Martin <che dot l dot martin at gmail dot com> Yoezen Hernandez <yzhernand at gmail dot com> Levy Vargas <levy dot vargas at gmail dot com> Weigang Qiu <weigang at genectr dot hunter dot cuny.edu> (Maintainer)
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.