alignment-gild1

Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.

Usage

alignment-gild alignment-file tree-file alignments-file [alignments-file] [OPTIONS]

Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.

`-h, –help`	produce help message
`–align arg`	file with alignment to annotate
`–tree arg`	file with tree
`–find-root`	estimate the root position from branch lengths
`–alphabet arg`	set to `Codons' to prefer codon alphabets
`–skip arg (=0)`	number of alignment samples to skip
`–max-alignments arg (=1000)`	maximum number of alignments to analyze
`-V, –verbose`	Output more log messages on stderr.

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .

Please send bug reports to ⟨[email protected]⟩\c .

4 releases since Debian 10 (Buster); the text changed 2 times.