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

# indelFit(1)

Estimate the parameters of a simple indel model, given an indel history

## NAME

indelFit - Estimate the parameters of a simple indel model, given an indel history

## DESCRIPTION

Estimate the parameters of a simple indel model, given an indel history and a tree.  By default, writes estimates of three parameters to stdout: an insertion rate alpha, a deletion rate beta, and a parameter tau roughly equal to the inverse of the expected indel length (modulo adjustments required to make probabilities sum to one).

-

  An indel history can be obtained with indelHistory and a tree with phyloFit.

## OPTIONS

**--alpha**, **-a** \<val\>

- Starting value of alpha, the insertion rate.

  Default is 0.02.

**--beta**, **-b** \<val\> Starting value of beta, the deletion rate. Default is 0.04.

**--tau**, **-t** \<val\> Starting value of tau, the length parameter. Default is 0.05.

**--lnl**, **-L**

-

  Compute log likelihood of model only, without optimizing parameters. The options above can be used to set the parameters as desired.

**--columns**, **-c**

-

  Output log likelihood of each column.

**--features**, **-f** \<file.gff\>

-

  Estimate separate parameters for each type of feature in the given file, as well as for background sites.

**--reference**, **-r** \<name\>

-

  (For use with **--features**) Name of species (node of tree) defining coordinate frame of features.  By default, the coordinate frame of the entire alignment is assumed.

**--log**, **-l** \<file\>

-

  Write log of optimization to specified file.

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

-

  Display this help message and exit.