NAME
alignment-gild - Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.
SYNOPSIS
alignment-gild alignment-file tree-file alignments-file [alignments-file] [OPTIONS]
DESCRIPTION
Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.
ALLOWED OPTIONS:
- -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.
REPORTING BUGS:
BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
AUTHORS
Benjamin Redelings.