Man page - alignment-cat(1)
Packages contas this manual
- alignment-distances(1)
- alignment-max(1)
- bali-phy(1)
- tree-mean-lengths(1)
- mcon-tool(1)
- extract-ancestors(1)
- cut-range(1)
- alignment-indices(1)
- alignment-thin(1)
- stats-select(1)
- pickout(1)
- trees-consensus(1)
- alignment-gild(1)
- alignment-chop-internal(1)
- summarize-ancestors(1)
- draw-tree(1)
- bali-phy-pkg(1)
- mctree-mean-lengths(1)
- tree-tool(1)
- alignment-find(1)
- trees-bootstrap(1)
- alignment-translate(1)
- trees-distances(1)
- alignment-cat(1)
- statreport(1)
- bp-analyze(1)
- alignment-info(1)
- alignment-draw(1)
- alignments-diff(1)
- alignment-consensus(1)
- bali-subsample(1)
Package: bali-phy
apt-get install bali-phy
apt-get install bali-phy
Manuals in package:
Documentations in package:
Manual
| alignment-cat(1) | alignment-cat(1) |
NAME
alignment-cat - Concatenate several alignments (with the same sequence names) end-to-end.
SYNOPSIS
alignment-cat file1 [file2 ...]
DESCRIPTION
Concatenate several alignments (with the same sequence names) end-to-end.
ALL OPTIONS:
- -h, –help
- Produce help message
- –output arg (=fasta)
- Which output format: fasta or phylip?
- -c arg, –columns arg
- Ranges of columns to keep, like: 1-10,30-
- -t arg, –taxa arg
- Taxa to keep, comma-separated
- -p, –pad
- Add gaps to make sequence lengths identical
- -r, –reverse
- Reverse the sequences
- -e, –erase-empty-columns
- Remove columns with no characters (all gaps).
- –missing arg (=-?)
- What letters are not characters (e.g. gaps)?
- –strip-gaps
- Remove all non-character letters from sequences.
- –reorder-by-tree arg
- Reorder the sequences given a tree
- –use-root
- use the root specified in the tree file to reorder
- –reorder-by-alignment arg
- Reorder the sequences following an alignment
- –align-by-amino arg
- Arrange nucleotides into codon alignment
EXAMPLES:
To select columns from an alignment:
-
% alignment-cat -c1-10,50-100,600- filename.fasta > result.fasta % alignment-cat -c5-250/3 filename.fasta > first_codon_position.fasta % alignment-cat -c6-250/3 filename.fasta > second_codon_position.fasta
To concatenate two or more alignments:
-
% alignment-cat filename1.fasta filename2.fasta > all.fasta
REPORTING BUGS:
BAli-Phy online help: http://www.bali-phy.org/docs.php.
Please send bug reports to bali-phy-users@googlegroups.com.
AUTHORS
Benjamin Redelings.
| Feb 2018 |