GenomeTools

To load this software in a Linux environment run the commands:

module load genometools

To use a software tool contained in GenomeTools, such as LTRharvest, enter the command:

gt ltrharvest <input_commands>

Here ltrharvest is used as an example of one possible software tool, and <input_commands> stands for the appropriate input commands the user has chosen for use with the tool.

To obtain a list of all tools in GenomeTools, enter the command

gt -help

The individual tools implement a -help option. For example, to learn the options accepted by LTRharvest, enter the command:

gt ltrharvest -help

The software tools included in GenomeTools are:

• ltrharvest  -  an efficient and flexible software tool for de novo detection of LTR retrotransposons.
• tallymer  -  a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
• uniquesub  -  a program for computing minimum unique substrings.
• AnnotationSketch  -  a library for drawing genome annotations.
• ltrdigest  -  a software tool for automated annotation of internal features of LTR retrotransposons.
• MetaGenomeThreader  -  a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects.
• GtEncseq  -  a compressed biosequence representation with many features.
• Readjoiner  -  a sequence assembler based on the assembly string graph framework.

GenomeTools is freely availabe at http://genometools.org/ .  This website also contains information on the included software tools and their use.