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authorPetar Petrov <petar.petrov@student.oulu.fi>2014-10-01 09:11:46 +0700
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2014-10-03 10:16:55 +0700
commitd8d998a60208db638c7c5846df51ef0c4557aeb5 (patch)
tree564a89aa5f3bd1b56e69e35daed1a1374b5d3056 /academic/ugene/README
parent33ad3c32e1608af653595113b49ebe4dde7a959c (diff)
downloadslackbuilds-d8d998a60208db638c7c5846df51ef0c4557aeb5.tar.gz
academic/ugene: Updated for version 1.14.1.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/ugene/README')
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1 files changed, 6 insertions, 4 deletions
diff --git a/academic/ugene/README b/academic/ugene/README
index 4d1fc9662b..74e8a62736 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)