---
name: "alignment-thin"
section: "1"
platform: "linux"
package: "bali-phy"
version: "4.0-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/alignment-thin"
---

# alignment-thin(1)

Remove sequences or columns from an alignment.

## NAME

**alignment-thin** - Remove sequences or columns from an alignment.

## SYNOPSIS

**alignment-thin** *alignment-file* \[OPTIONS\]

## DESCRIPTION

Remove sequences or columns from an alignment.

## GENERAL OPTIONS:

- **-h**, **–help**

  Print usage information.

- **-V**, **–verbose**

  Output more log messages on stderr.

## SEQUENCE FILTERING OPTIONS:

- **-p** *arg*, **–protect** *arg*

  Sequences that cannot be removed (comma-separated).

- **-k** *arg*, **–keep** *arg*

  Remove sequences not in comma-separated list *arg*.

- **-r** *arg*, **–remove** *arg*

  Remove sequences in comma-separated list *arg*.

- **-l** *arg*, **–longer-than** *arg*

  Remove sequences not longer than *arg*.

- **-s** *arg*, **–shorter-than** *arg*

  Remove sequences not shorter than *arg*.

- **-c** *arg*, **–cutoff** *arg*

  Remove similar sequences with #mismatches \< cutoff.

- **-d** *arg*, **–down-to** *arg*

  Remove similar sequences down to *arg* sequences.

- **–remove-gappy** *arg*

  Remove *arg* outlier sequences – defined as sequences that are missing too many conserved sites.

- **–conserved** *arg* (=0.75)

  Fraction of sequences that must contain a letter for it to be considered conserved.

## COLUMN FILTERING OPTIONS:

- **-K** *arg*, **–keep-columns** *arg*

  Keep columns from this sequence

- **-m** *arg*, **–min-letters** *arg*

  Remove columns with fewer than *arg* letters.

- **-u** *arg*, **–remove-unique** *arg*

  Remove insertions in a single sequence if longer than *arg* letters

- **-e**, **–erase-empty-columns**

  Remove columns with no characters (all gaps).

## OUTPUT OPTIONS:

- **-S**, **–sort**

  Sort partially ordered columns to group similar gaps.

- **-L**, **–show-lengths**

  Just print out sequence lengths.

- **-N**, **–show-names**

  Just print out sequence lengths.

- **-F** *arg*, **–find-dups** *arg*

  For each sequence, find the closest other sequence.

## EXAMPLES:

Remove columns without a minimum number of letters:

-

  ```
  % alignment-thin --min-letters=5 file.fasta > file-thinned.fasta
  ```

Remove sequences by name:

-

  ```
  % alignment-thin --remove=seq1,seq2 file.fasta > file2.fasta
  ```

-

  ```
  % alignment-thin --keep=seq1,seq2   file.fasta > file2.fasta
  ```

Remove short sequences:

-

  ```
  % alignment-thin --longer-than=250 file.fasta > file-long.fasta
  ```

Remove similar sequences with \<= 5 differences from the closest other sequence:

-

  ```
  % alignment-thin --cutoff=5 file.fasta > more-than-5-differences.fasta
  ```

Remove similar sequences until we have the right number of sequences:

-

  ```
  % alignment-thin --down-to=30 file.fasta > file-30taxa.fasta
  ```

Remove dissimilar sequences that are missing conserved columns:

-

  ```
  % alignment-thin --remove-gappy=10 file.fasta > file2.fasta
  ```

Protect some sequences from being removed:

-

  ```
  % alignment-thin --down-to=30 file.fasta --protect=seq1,seq2 > file2.fasta
  ```

-

  ```
  % alignment-thin --down-to=30 file.fasta --protect=@filename > file2.fasta
  ```

## REPORTING BUGS:

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\\c .

Please send bug reports to ⟨bali-phy-users@googlegroups.com⟩\\c .

## AUTHORS

Benjamin Redelings.