---
name: "indelHistory"
section: "1"
platform: "linux"
package: "phast"
version: "1.7+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/indelHistory"
---

# indelHistory(1)

Obtain an "indel history" for an alignment and write it to a file

## 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

**--msa-format**, **-i** FASTA\|MAF\|SS\|....

-

  Read alignment in specified file format (default FASTA).

**--output-alignment**, **-A**

-

  Instead of a summary of indels only, output an alignment in FASTA format of sequences for all ancestral and leaf nodes.

**--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.

**--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".

**--help**, **-h**

-

  Display this help message.