NAME

alignment-chop-internal - Remove ancestral sequences from FASTA alignment samples.

SYNOPSIS

alignment-chop-internal -N count < alignments-file > leaves.fastas

alignment-chop-internal --tree tree-file < alignments-file > leaves.fastas

DESCRIPTION

Read FASTA alignments from standard input and write selected sequences from each alignment to standard output. Read input through shell redirection or a pipe; there is no positional input filename.

Choose exactly one selection method: retain the first N sequences with --nleaves, or retain sequences whose names occur as leaves in --tree. Ancestral sequences are not identified from their contents.

Each input alignment begins with a FASTA header whose first character is > and ends at an empty line or end of input. Separate successive alignments with empty lines. Text before or between alignment blocks is skipped while looking for the next header. Output alignments are in FASTA format, separated by empty lines.

Sequence names are the text after > up to the first space or tab; the remaining header text is a comment. Letters are converted to uppercase, but sequence names retain their case. Retained sequences keep their input order and columns, including columns containing only gaps. The tool does not interpret a sequence alphabet or require equal sequence lengths.

OPTIONS

-h, --help

Print usage information and exit.

-N count, --nleaves count

Keep the first count sequences in each alignment. This assumes the desired leaf sequences precede ancestral sequences. A count of zero produces no sequences. An alignment with fewer than count sequences causes an error. Cannot be combined with --tree.

--tree tree-file

Read the first tree from a Newick or NEXUS file and keep sequences whose names match its leaf labels. Matching is case-sensitive. Internal-node labels and branch lengths do not affect selection. Output follows alignment order, not tree order. Cannot be combined with --nleaves. Empty leaf labels are ignored with a warning; duplicate nonempty leaf labels cause an error. An alignment with fewer sequences than the number of distinct nonempty leaf labels also causes an error. Otherwise, selection keeps every sequence whose name matches a leaf label: it does not check that every leaf occurs in the alignment or that alignment sequence names are unique.

EXAMPLES

Keep the first five sequences in every sampled alignment:

alignment-chop-internal -N 5 < samples.fastas > leaves.fastas

Keep sequences named by the leaves of a reference tree:

alignment-chop-internal --tree reference.tree < samples.fastas > leaves.fastas

Select the last alignment, then retain its leaf sequences:

alignment-find < samples.fastas | alignment-chop-internal --tree reference.tree > leaves.fasta

EXIT STATUS

Returns 0 on success (including --help) and 1 when an error is reported. Warnings and error messages are written to standard error. Input containing no alignment blocks produces no output and succeeds, provided the selection options and any tree input are valid. If a later alignment fails, output from earlier alignments may already have been written.

SEE ALSO

alignment-find(1), alignment-cat(1), cut-range(1)

REPORTING BUGS

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.