---
name: "slice_mercator_alignment"
section: "1"
platform: "linux"
package: "fsa"
version: "1.15.9+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/slice_mercator_alignment"
---

# slice\_mercator\_alignment(1)

Extracts the corresponding subalignment from a Mercator multiple alignment

## NAME

slice\_mercator\_alignment - Extracts the corresponding subalignment from a Mercator multiple alignment

## SYNOPSIS

**slice\_mercator\_alignment** \[*options*\] *\<genome\> \<chromosome\> \<start\> \<end\> \<strand\>*

## DESCRIPTION

slice\_mercator\_alignment from FSA 1.15.9

Extracts the corresponding subalignment from a Mercator multiple alignment.

## OPTIONS

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

  show this message

- **-D**, **--data** \<directory\>

  path to map, genome and alignment files

- **-M**, **--map** \<directory\>

  path to map and genome files

- **-A**, **--align** \<directory\>

  path to alignment files

- **-L**, **--lazy**

  warn, rather than die, if the subalignment can't be obtained

- **-U**, **--truncate**

  truncate unmappable sequence (rather than skipping) and show truncated subalignment

- **-s**, **--stockholm**

  use and display Stockholm-format alignments with conservation statistics (default is multi-FASTA)

- **-0**, **--zerobased**

  coordinates are 0-based (default is 1-based)

- **-o**, **--halfopen**

  end coordinate is open, i.e., \[start, end)

Assumes that coordinates are 1-based and fully-closed, therefore representing the interval \[start, end\].

If requested, unmappable sequence will be truncated to the mappable portion; note that the truncation will favor the beginning of the requested sequence.

If the requested sequence is on the - strand, then the corresponding subalignment will be reverse-complemented.

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.