SAM alignment file
File type: Various data file
A PA2M file is an alignment file used by the SAM (Sequence Alignment and Modeling system). It stores aligned sequences in sequence format together with posterior probability annotations.
The file is created by pathprobs as part of SAM's alignment-processing workflow.
File type category:
Various data file
Date updated: September 27, 2026
SAM is bioinformatics software for sequence alignment and modeling. A PA2M file contains alternating sequence data and posterior probability annotations, keeping an alignment and its associated probability information together.
The format is intended for use with SAM's pathprobs tool and related alignment-processing workflow. SAM is available on Linux and Unix systems.
Open a PA2M file with the SAM software on Linux or Unix, using SAM tools that support the output produced by pathprobs. A text editor can display the file's sequence-format contents, but it will not interpret the alignment or posterior probability annotations.
If another alignment format is needed, a SAM utility or a custom script must parse the sequence and posterior probability data and write the target format.
Conversion may discard the posterior probability annotations if the target format does not support them.
Software applications that handle other tasks involving pa2m files:
Linux/Unix
Language
