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Diffstat (limited to 'academic/ugene/README')
| -rw-r--r-- | academic/ugene/README | 17 |
1 files changed, 7 insertions, 10 deletions
diff --git a/academic/ugene/README b/academic/ugene/README index b0a0c8064c..181b318651 100644 --- a/academic/ugene/README +++ b/academic/ugene/README @@ -38,28 +38,25 @@ program. All of them are available at SlackBuilds.org: - 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-conductGO (Find the top-n highest expressed TFs) -- cistrome-extra (Cistrome Applications Harvard extra apps) -- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq) -- cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos) -- clark-ugene (Ugene's forked CLAssifier based on Reduced K-mers) - clustalo (Clustal Omega) - clustalw (Multiple Sequence Alignment) - cufflinks (A reference-guided assembler for RNA-Seq experiments) - cutadapt (Trim adapters from high-throughput sequencing reads) -- diamond (A sequence aligner for protein and translated DNA) - fastqc (A quality control tool for high throughput sequence data) +- FastTree (Infers approximately-ML phylogenetic trees) - HMMER (Biosequence analysis using profile hidden Markov models) -- kraken (Assign taxonomic labels to short DNA sequences) -- MetaPhlAn (Metagenomic Phylogenetic Analysis) -- ncbi-blast (BLAST: Basic Local Alignment Search Tool) +- iqtree (Efficient and versatile phylogenomic software by ML) +- kalign (A fast multiple sequence alignment program) +- MetaPhlAn2 (Metagenomic Phylogenetic Analysis) +- mafft (A multiple sequence alignment program) +- mrbayes (MrBayes: Bayesian Inference of Phylogeny) - ncbi-blast+ (BLAST+ Command Line Applications) - PhyML (Phylogenetic estimation using Maximum Likelihood) - samtools-legacy (Sequence Alignment/Map Tools) - snpEff (Genetic variant annotation and effect prediction toolbox) - spades (SPAdes Genome Assembler) - spidey (mRNA-to-genomic alignment) +- stringtie (Assembler of RNA-Seq alignments) - t_coffee (A multiple sequence alignment program) - tabix-legacy (Generic indexer for TAB-delimited genome position files) - tophat (Splice junction mapper for RNA-Seq reads) |