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

# convert\_coords(1)

converts coordinates of features in a GFF file according to a multiple alignment

## NAME

convert\_coords - converts coordinates of features in a GFF file according to a multiple alignment

## DESCRIPTION

Converts coordinates of features in a GFF file according to a multiple alignment.  Will map from the coordinate system of any sequence to any other sequence; can also map to or from the coordinate system of the entire alignment.  In addition, supports translation of coordinates by specified offset.

## OPTIONS

- **-m** \<msa\_fname\>

  (required) Name of file in which alignment is defined.

- **-f** \<gff\_fname\>

  (required) Name of file in which features are defined (GFF).

- **-s** \<src\_frame\>

  Index of frame of reference for feature coordinates, as defined in the GFF file.  Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole.  Default behavior is to match features with alignment sequences by name (feature by feature). **-d** \<dest\_frame\> Index of destination frame of reference. Default is 0 (whole MSA). **-p** \<coord\_off\> Positive coordinate offset.  This value will be added to all coordinates.  Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. **-n** \<coord\_off\> Negative coordinate offset.  This value will be subtracted from all coordinates.  Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. **-i** FASTA\|PHYLIP\|MPM\|SS Alignment format.  Default is to guess format from file contents