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Diffstat (limited to 'academic/ugene/README')
| -rw-r--r-- | academic/ugene/README | 10 |
1 files changed, 6 insertions, 4 deletions
diff --git a/academic/ugene/README b/academic/ugene/README index 4d1fc9662bb38..74e8a62736fa9 100644 --- a/academic/ugene/README +++ b/academic/ugene/README @@ -21,23 +21,25 @@ be launched on local resources or in a High Performance Computing built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. -IMPORTANT: External tools +EXTERNAL TOOLS UGENE can use and drive a number of external tools, providing a nice and unified GUI. These are not needed at build time, but are highly recommended for the complete (and extended) functionality of the program. Almost all of them can be found at SlackBuilds.org: -- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System) -- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq) -- cufflinks (A reference-guided assembler for RNA-Seq experiments) +- bedtools (A powerful toolset for genome arithmetic) - bowtie (A short read aligner of DNA sequences) - bowtie2 (A tool for aligning sequencing reads) - bwa (Burrows-Wheeler Aligner) - cap3 (CAP3: A DNA sequence assembly program) +- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System) +- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq) - clustalo (Clustal Omega) - clustalw (Multiple Sequence Alignment) +- cufflinks (A reference-guided assembler for RNA-Seq experiments) - ncbi-blast (BLAST: Basic Local Alignment Search Tool) - ncbi-blast-plus (BLAST+ Command Line Applications) +- PhyML (Phylogenetic estimation using Maximum Likelihood) - samtools (Sequence Alignment/Map Tools) - spidey (mRNA-to-genomic alignment) - t_coffee (A multiple sequence alignment program) |