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LAST-TRAIN

Improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. LAST-TRAIN uses a standard iterative approach: it first aligns the sequences using some initial score parameters, then infers better score parameters from the alignments, then re-aligns and repeats until the parameters stop changing. It achieves adequate speed by an X-drop heuristic, depletes paralogs using LASTSPLIT, and allows different insertion and deletion parameters and non-strand-symmetric substitution parameters.

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LAST-TRAIN classification

LAST-TRAIN specifications

Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable

LAST-TRAIN distribution

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No open topic.

LAST-TRAIN classification

LAST-TRAIN specifications

Interface:
Web user interface
Computer skills:
Basic
Maintained:
Yes
Restrictions to use:
None
Stability:
Stable

LAST-TRAIN support

Documentation

Maintainer

  • Martin Frith <>
  • Martin Frith <>

Credits

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Publications

Institution(s)

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan; Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan; IMSBIO Co, Ltd, Tokyo, Japan; Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan

Funding source(s)

This work was supported by MEXT KAKENHI [grant numbers JP24680031, JP16H05879, JP16H01318, JP26700030, JP25240044, JP221S0002].

Link to literature

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