ltrsift (1)

A graphical interface for postprocessing and classification of ltr retrotransposon candidates

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  4. ltrsift: A graphical interface for postprocessing and classification of ltr retrotransposon candidates
  1. Carta.tech
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  3. ltrsift
  4. ltrsift: A graphical interface for postprocessing and classification of ltr retrotransposon candidates

SYNOPSIS

ltrsift

DESCRIPTION

LTRsift is a graphical desktop tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations, such as the ones generated by LTRharvest and LTRdigest.

CONFIGURATION

The LAST binaries (lastal and lastdb) should be located in the system search path. If they are not, is it possible to specify their location using the “GT_LAST_PATH" environment variable prior to running LTRsift. The same applies for the BLAST location. Use ``GT_BLAST_PATH” to specify the the full path to the “blastall” executable.

Style files (describing how the linear diagram of the candidate features look like) can be set via the LTRSIFT_STYLE_FILE environment variable. A sensible default style is built into LTRsift.

AUTHOR

Report bugs to <[email protected]>.