---
name: "Bio::AlignIO::largemultifasta"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::AlignIO::largemultifasta"
---

# Bio::AlignIO::largemultifasta(3pm)

Largemultifasta MSA Sequence input/output stream

## NAME

Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence input/output stream

## SYNOPSIS

Do not use this module directly.  Use it via the Bio::AlignIO class.

## DESCRIPTION

This object can transform Bio::SimpleAlign objects to and from largemultifasta flat file databases.  This is for the fasta sequence format NOT FastA analysis program.  To process the pairwise alignments from a FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.

Reimplementation of Bio::AlignIO::fasta modules so that creates temporary files instead of keeping the whole sequences in memory.

## FEEDBACK

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

### Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the web:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHORS - Albert Vilella, Heikki Lehvaslaiho

Email: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org

## APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_

### next\_seq

```
 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream while taking care
           of the length
 Returns : Bio::Seq object
 Args    : NONE
```

### next\_aln

```
 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
        or on error
 Args    : NONE
```

### write\_aln

```
 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in largemultifasta format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object
```