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Sequence Alignment and Modeling system

Found 29 file extension associations related to Sequence Alignment and Modeling system and 26 file formats developed specifically for use with Sequence Alignment and Modeling system.

Platform, operating system:  Linux/Unix icon Linux/Unix

Go to: Sequence Alignment and Modeling system description

Developer: Richard Hughey - Kevin Karplus - Anders Krogh

Richard Hughey - Kevin Karplus - Anders Krogh software list & details

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Sequence Alignment and Modeling system

Developer / company: Richard Hughey - Kevin Karplus - Anders Krogh

The Sequence Alignment and Modeling system (SAM) is a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. The model states can be viewed as representing the sequence of columns in a multiple sequence alignment, with provisions for arbitrary position-dependent insertions and deletions in each sequence. The models are trained on a family of protein or nucleic acid sequences using an expectation-maximization algorithm and a variety of algorithmic heuristics. A trained model can then be used to both generate multiple alignments and search databases for new members of the family.

SAM includes programs and scripts for the SAM-T99 method of remote homology detection. SAM-T99 is an iterative HMM search method for creating an HMM from a single protein sequence or seed alignment using iterative search of a protein database. The method is currently the most sensitive purely-sequence-based remote homology detection algorithm. SAM-T99 is based on successful methods created for the CASP2 and CASP3 protein structure prediction experiments.

The Sequence Alignment and Modeling system software seems to be old or discontinued.
Such programs may not work on modern operating systems properly, are no longer available and supported by their original developers, or are simply obsolete for their purpose. Sometimes companies offer limited support through their website.

Sequence Alignment and Modeling system works with the following file extensions:

Note: You can click on any file extension link from the list below, to view its detailed information. The list of extensions used or otherwise associated with the application may not be complete, because many common file extensions on our website, such as jpg (pictures) or txt (text files), can be opened by a large number of applications, or are too general file format. However most, if not all directly associated file extensions should be listed with its appropriate program. Although its likely, that some file extensions may be missing from the list of associated file extensions with the application, yet they can be opened, be part of, or otherwise be associated with the program.

Sequence Alignment and Modeling system default file extension associations

a2m file icon.a2mapr file icon.aprcolors file icon.colorscst file icon.cstdata file icon.datadist file icon.distfreq file icon.freqhmmer file icon.hmmerhmmr file icon.hmmrkids file icon.kidskseqs file icon.kseqsmatch-rdb file icon.match-rdbmlib file icon.mlibmstat file icon.mstatmult file icon.multncomp file icon.ncomppa2m file icon.pa2mpdoc file icon.pdocplib file icon.plibpretty file icon.prettyptrack file icon.ptrackregularizer file icon.regularizersamrc file icon.samrcstat file icon.statweightoutput file icon.weightoutputweights file icon.weights

Other file extensions associated with Sequence Alignment and Modeling system

mod file icon.modsel file icon.selseq file icon.seq

Comparison table of actions that Sequence Alignment and Modeling system can perform with each of its associated file type beta

This table might not contain all possible associated or supported file types or may contain incorrect data.
If you need more information please contact the developers of Sequence Alignment and Modeling system (Richard Hughey - Kevin Karplus - Anders Krogh), or check out their product website.

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a2m

---------------YesYes

apr

---------------YesYes

colors

----------------Yes

cst

YesYesYes---Yes----------

data

----------------Yes

dist

----------------Yes

freq

------Yes---------Yes

hmmer

YesYesYes---Yes----------

hmmr

------Yes---------Yes

kids

------Yes---------Yes

kseqs

------Yes---------Yes

match-rdb

----------------Yes

mlib

----------------Yes

mod

Yes---------------Yes

mstat

------Yes---------Yes

mult

------Yes---------Yes

ncomp

----------------Yes

pa2m

----------------Yes

pdoc

YesYesYes---Yes---------Yes

plib

----------------Yes

pretty

------Yes---------Yes

ptrack

----------------Yes

regularizer

----------------Yes

samrc

----------------Yes

sel

----------------Yes

seq

YesYesYes---Yes----------

stat

------Yes---------Yes

weightoutput

----------------Yes

weights

----------------Yes

 

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