5. Information of the used prerequisite tools > Manual

TGFam-Finder provides an automatic install script, but if you want to use TGFam-Finder through already installed programs, you should install the following programs.

List of programs used in TGFam-Finder

If you do not want Auto Installation, or if you are using the self-installer, you need to install the program below to use TGFam-Finder.

Bioperl
Homepage: https://bioperl.org/index.html

Manual: https://bioperl.org/INSTALL.html

 

Bowtie2

Homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Manual: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

TGFam-Finder Current Version: 2.3.1-x86_64

 

Samtools

Homepage: http://www.htslib.org/

Manual: http://www.htslib.org/doc/#manual-pages

TGFam-Finder Current Version: 0.1.19-x86_64

 

Hmmer

Homepage: http://hmmer.org/

Manual: http://hmmer.org/documentation.html

TGFam-Finder Current Version: 3.1b2-x86_64

 

BLAST+

Homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/

TGFam-Finder Current Version: 2.6.0+-x86_64

 

Exonerate

Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Manual: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate-user-guide

TGFam-Finder Current Version: 2.2.0-x86_64

 

Tophat

Homepage: https://ccb.jhu.edu/software/tophat/index.shtml

Manual: https://ccb.jhu.edu/software/tophat/manual.shtml

TGFam-Finder Current Version: 2.1.1-x86_64

 

Cufflinks

Homepage: http://cole-trapnell-lab.github.io/cufflinks/

Manual: https://github.com/cole-trapnell-lab/cufflinks

TGFam-Finder Current Version: 2.2.1-x86_64

 

Scipio

Homepage: http://www.webscipio.org/

Manual: https://www.webscipio.org/webscipio/download_scipio

TGFam-Finder Current Version: scipio-1.4

 

Augustus

Homepage: http://bioinf.uni-greifswald.de/augustus/

Manual: http://bioinf.uni-greifswald.de/augustus/

TGFam-Finder Current Version: augustus-3.2.3

 

Blat

Homepage: http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

Manual: http://genome.ucsc.edu/goldenPath/help/blatSpec.html

TGFam-Finder Current Version: 35

 

ClustalW

Homepage: http://www.clustal.org/clustal2/

Manual: http://www.clustal.org/clustal2/#Documentation

TGFam-Finder Current Version: 2.1

 

InterProScan

Homepage: https://www.ebi.ac.uk/interpro/

Manual: https://www.ebi.ac.uk/interpro/documentation.html

TGFam-Finder Current Version: 5.22-61-64bit