---
name: "homology-score.pl"
section: "1"
platform: "linux"
package: "murasaki-common"
version: "1.68.6-14"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/homology-score.pl"
---

# homology-score.pl(1)

generates homology scorse from murasaki anchor files

## NAME

homology-score.pl - generates homology scorse from murasaki anchor files

## SYNOPSIS

filter.pl \[options\] \<murasaki ailgnment file\> \[output file\]

## OPTIONS

```
 --aligner=<alignment program> => Selects the aligner program.
     Options are clustalw (slow but won't die on large anchors),
     or muscle (fast, but dies on anchors longer than 20k).
     Default is Muscle.
```