indelHistory(1)
Obtain an "indel history" for an alignment and write it to a file
Description
INDELHISTORY
NAME
indelHistory - Obtain an "indel history" for an alignment and write it to a file
DESCRIPTION
Obtain an "indel history" for an alignment and write it to a file describing insertions and deletions in all species using a compact format. The specified alignment may either contain sequences corresponding only to leaves of the specified tree, in which case an indel history will be inferred using a simple parsimony algorithm, or it may contain sequences for all nodes in the tree, in which case the indel history will simply be extracted from the file.
OPTIONS
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--msa-format, -i FASTA|MAF|SS|.... |
Read alignment in specified file format (default FASTA).
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--output-alignment, -A |
Instead of a summary of indels only, output an alignment in FASTA format of sequences for all ancestral and leaf nodes.
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--read-history, -H <fname> Read an indel history directly from the specified file. Useful for debugging. The alignment and tree arguments are not required; |
however in an alignment is given with --read-history and --output-alignment, then actual bases can be output for leaf species.
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--ia-names, -I |
Assume ancestral sequences in alignment.fa are named according to the convention used by Mathieu Blanchette’s inferAncestors program, e.g., "RAT+MOUSE+RABBIT+" for the last common ancestor of "rat", "mouse", and "rabbit".
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--help, -h |
Display this help message.