Changes between Version 92 and Version 93 of Software

Timestamp:

Sep 10, 2021, 9:48:21 AM (3 years ago)

Author:

ausa0001

Comment:

--

Software

@@ -9 +9 @@
   * [[Software/Bowtie2]] - Fast short read aligner
   * [[Software/NCBI-BLAST+]] - Local sequence alignment search tool 
-  * [[Software/Diamond]] - Sequence aligner for protein and translated DNA searches (Version 0.9.26)
+  * [[Software/Diamond]] - Sequence aligner for protein and translated DNA searches
   * [[Software/Exonerate]] - Sequence alignment tool, excels e.g. at spliced EST alignments
   * [[Software/Infernal]] - Inference of RNA alignments
   * [[Software/GmapGsnap]] - GMAP/GSNAP short read mapper/aligner for RNASeq and genomic data
-  * [[Software/Mafft]] - Multiple sequence alignment program (Version 7.450)
+  * [[Software/Mafft]] - Multiple sequence alignment program
   * [[Software/Mauve]] - Multiple alignment of genomes
   * [[Software/Salmon]] - RNASeq alignment and quantification tool
@@ -19 +19 @@
 
 === Classification
-  * [[Software/GraftM]] - Pipeline to identify and classify marker gene reads from metagenomic datasets (Version 0.13.1)
+  * [[Software/GraftM]] - Pipeline to identify and classify marker gene reads from metagenomic datasets
 
 === Graphs
@@ -26 +26 @@
 === Phylogeny
   * [[Software/CAFE]] - Evaluate gene family evolution within a species tree
-  * [[Software/IQ-TREE]] - Efficient software for phylogenomic inference (Version 1.6.12)
-  * [[Software/FastTreeMP]] - Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. (Version 2.1.11)
-  * [[Software/OrthoFinder]] - Infers orthogroups, gene trees of orthogroups and species trees from proteomes. (Version 2.3.8)
-  * [[Software/Pplacer]] - Phylogenetic placement (Version 1.1.19)
-  * [[Software/gappa]] - Placements of short environmental sequences on a reference phylogenetic tree (Version 0.6.1)
+  * [[Software/IQ-TREE]] - Efficient software for phylogenomic inference
+  * [[Software/FastTreeMP]] - Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
+  * [[Software/OrthoFinder]] - Infers orthogroups, gene trees of orthogroups and species trees from proteomes.
+  * [[Software/Pplacer]] - Phylogenetic placement
+  * [[Software/epa-ng]] - Phylogenetic placement
+  * [[Software/gappa]] - Placements of short environmental sequences on a reference phylogenetic tree
   * [[Software/SEPP]] - SATe-enabled Phylogenetic Placement
   * [[Software/exabayes]] - Massively parallel Bayesian phylogenetic analysis
@@ -37 +38 @@
 === Sequence analysis
   * [[Software/BUSCO]] - Software package to evaluate genome completeness.
-   * [[Software/Fxtract]] - Extract sequences from a fastx file given a subsequence or identifier (Version 2.3)    
-  * [[Software/HMMER]] - Biosequence analysis using profile hidden Markov models (Version 3.2.1)  
-  * [[Software/OrfM]] - A simple and not slow open reading frame (ORF) caller (Version 0.7.1)
+   * [[Software/Fxtract]] - Extract sequences from a fastx file given a subsequence or identifier   
+  * [[Software/HMMER]] - Biosequence analysis using profile hidden Markov models  
+  * [[Software/OrfM]] - A simple and not slow open reading frame (ORF) caller
   * [[Software/RECON]] - Software for repeat finding in genomic sequences (please check Software/RepeatModeler)
   * [[Software/RepeatScout]] - Software for repeat find in genomic sequences  (please check Software/RepeatModeler)
@@ -45 +46 @@
   * [[Software/RepeatModeler]] - The de-novo repeat family identification and modeling package.
   * [[Software/TRF ]] - Software for finding tandem repeats in genomic sequences
-  * [[Software/mfqe ]] - FASTA/FASTQ extractor for multiple sets of read names (Version 0.5.0) 
+  * [[Software/mfqe ]] - FASTA/FASTQ extractor for multiple sets of read names
   * [[Software/BCFtools]] - Analysis and handling of VCF/BCF (Variant Call Format) files
   * [[Software/BEDtools]] - Swiss Army knife for genomic analysis
@@ -58 +59 @@
   * [[Software/Prodigal]] - Fast, reliable protein-coding gene prediction for prokaryotic genomes.
   * [[Software/SNAP]] - Semi-HMM-based Nucleic Acid Parser. A gene prediction tool.
-  * [[Software/tRNAScan-SE]] - Annotate tRNAs in DNA sequence (version 2.0.7)
+  * [[Software/tRNAScan-SE]] - Annotate tRNAs in DNA sequence
 
 === Assembly tools -- genome and transcriptome assembly
@@ -72 +73 @@
 
 === Statistics
-  * [[Software/R]] - The R language for statistical computing (Versions: 3.6.0)
+  * [[Software/R]] - The R language for statistical computing
 
 === Perl
-  * [[Software/Perl]] - The Perl programming language (Version 5.30.0)
+  * [[Software/Perl]] - The Perl programming language
 
 === Python