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 ... [OPTIONS] <
alignments-file
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 sequences and initial alignment
- --tree arg
- file with initial 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.
AUTHORS¶
Benjamin Redelings.