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

# simpal.pl(1)

## NAME

simpal -- proof of concept

## SYNOPSIS

simpal.pl \[options\] \<ref seq\> \<target seq\> \[target2 target3 ...\]

## OPTIONS

```
 Set options by something like --tolerance=5 or -t 5 or whatever.
maxLoop -- specifies max separation for the ends of the palindromes
maxDistance -- specifies the maximum difference in palindrome length
               when comparing palindromes
tolerance -- max permissible misses in palindromes between sequences
```

Setting either to -1 means no limit

seedlength -- length of seeds to use for finding palindromes