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general:computerenvironment:software:ecoevo_bioinf:softwarelist [2021/10/18 20:47] – [Software list] ingogeneral:computerenvironment:software:ecoevo_bioinf:softwarelist [2023/04/05 12:46] (current) – [Databases] freya
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 ===== Software list ===== ===== Software list =====
 Below you will find a diverse toolbox comprising numerous tools for the analysis of biological sequences. Not all of the tools will be used in the course, but maybe you are interested in taking a look around to see what is currently around.   Below you will find a diverse toolbox comprising numerous tools for the analysis of biological sequences. Not all of the tools will be used in the course, but maybe you are interested in taking a look around to see what is currently around.  
-^Type^Name^Description^GUI^Installation^URL|+^Type^Name^Description^%%GUI%%^Installation^%%URL%%|
 ^Read simulation|ART|Illumina, 454 and Solid read simulator|yes|[[https://bioconda.github.io/recipes/art/README.html|bioconda]]|[[https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm|Link]]| ^Read simulation|ART|Illumina, 454 and Solid read simulator|yes|[[https://bioconda.github.io/recipes/art/README.html|bioconda]]|[[https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm|Link]]|
 ^Read processing|FastQC|Generates summary statistics and overview information for DNA and RNA seq data|yes|[[https://anaconda.org/bioconda/fastqc|bioconda]]|[[https://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Link]]| ^Read processing|FastQC|Generates summary statistics and overview information for DNA and RNA seq data|yes|[[https://anaconda.org/bioconda/fastqc|bioconda]]|[[https://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Link]]|
 +| |SequelTools|Software package for the quality control, filtering and subread selection of PacBio reads|no|[[https://github.com/ISUgenomics/SequelTools#installation|manual]]|[[https://github.com/ISUgenomics/SequelTools|Link]]|
 | |Trimmomatic|Adapter clipping and quality trimming of short read data|no|[[https://anaconda.org/bioconda/trimmomatic|bioconda/conda-forge]]|[[http://www.usadellab.org/cms/?page=trimmomatic|Link]]| | |Trimmomatic|Adapter clipping and quality trimming of short read data|no|[[https://anaconda.org/bioconda/trimmomatic|bioconda/conda-forge]]|[[http://www.usadellab.org/cms/?page=trimmomatic|Link]]|
 ^Transcriptome assembly|Trinity|De novo reconstruction of transcriptomes from RNA-seq data|no|[[https://anaconda.org/bioconda/trinity|bioconda]]|[[https://github.com/trinityrnaseq/trinityrnaseq/wiki|Link]]| ^Transcriptome assembly|Trinity|De novo reconstruction of transcriptomes from RNA-seq data|no|[[https://anaconda.org/bioconda/trinity|bioconda]]|[[https://github.com/trinityrnaseq/trinityrnaseq/wiki|Link]]|
-^Genome assembly|Flye|ast and accurate de novo assembler for single molecule sequencing reads (suitable for PacBio HiFi reads)| no |[[https://anaconda.org/bioconda/flye]]|[[https://github.com/fenderglass/Flye|Link]]+^Genome assembly|Flye| Fast and accurate de novo assembler for single molecule sequencing reads (suitable for PacBio HiFi reads)|no|[[https://anaconda.org/bioconda/flye|bioconda]]|[[https://github.com/fenderglass/Flye|Link]]|
 | |CANU  |Assembler for High Noise / single molecule sequencing data (Overlap)  |no  |[[https://anaconda.org/bioconda/canu|bioconda]]|[[https://github.com/marbl/canu|Link]]  | | |CANU  |Assembler for High Noise / single molecule sequencing data (Overlap)  |no  |[[https://anaconda.org/bioconda/canu|bioconda]]|[[https://github.com/marbl/canu|Link]]  |
 | |Velvet  |Sequence assembler for short reads (deBruijn graph)|no  |[[https://anaconda.org/bioconda/velvet|bioconda]]|[[https://www.ebi.ac.uk/~zerbino/velvet/|Link]]  | | |Velvet  |Sequence assembler for short reads (deBruijn graph)|no  |[[https://anaconda.org/bioconda/velvet|bioconda]]|[[https://www.ebi.ac.uk/~zerbino/velvet/|Link]]  |
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 | |Diamond|Accelerated BLAST compatible local sequence aligner|no|[[https://anaconda.org/bioconda/diamond|bioconda]]|[[https://github.com/bbuchfink/diamond|Link]]| | |Diamond|Accelerated BLAST compatible local sequence aligner|no|[[https://anaconda.org/bioconda/diamond|bioconda]]|[[https://github.com/bbuchfink/diamond|Link]]|
 ^Gene prediction|maker|A comprehensive pipeline for genome annotation|no|[[https://anaconda.org/bioconda/maker|bioconda]]|[[http://www.yandell-lab.org/software/maker.html|Link]]| ^Gene prediction|maker|A comprehensive pipeline for genome annotation|no|[[https://anaconda.org/bioconda/maker|bioconda]]|[[http://www.yandell-lab.org/software/maker.html|Link]]|
-| |funannotate|A pipeline for gene annotation in fungal genomes|[[https://anaconda.org/bioconda/funannotate|bioconda]]|[[https://github.com/nextgenusfs/funannotate|link]]|+| |funannotate|A pipeline for gene annotation in fungal genomes|no|[[https://anaconda.org/bioconda/funannotate|bioconda]]|[[https://github.com/nextgenusfs/funannotate|link]]|
 | |Transdecoder|Identify candidate coding regions within transcript sequences|no|[[https://anaconda.org/bioconda/transdecoder|bioconda]]|[[https://github.com/TransDecoder/TransDecoder/wiki|Link]]| | |Transdecoder|Identify candidate coding regions within transcript sequences|no|[[https://anaconda.org/bioconda/transdecoder|bioconda]]|[[https://github.com/TransDecoder/TransDecoder/wiki|Link]]|
 ^Gene set completeness|Busco|Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs|no|[[https://anaconda.org/bioconda/busco|bioconda]]|[[https://busco.ezlab.org/|Link]]| ^Gene set completeness|Busco|Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs|no|[[https://anaconda.org/bioconda/busco|bioconda]]|[[https://busco.ezlab.org/|Link]]|
-| |fCAT|Gene set completeness assessment tool using domain-architecture aware targeted ortholog searches|[[https://github.com/BIONF/fcat#how-to-install|pip]] |[[https://github.com/BIONF/fcat|link]]|+| |fCAT|Gene set completeness assessment tool using domain-architecture aware targeted ortholog searches|no|[[https://github.com/BIONF/fcat#how-to-install|pip]] |[[https://github.com/BIONF/fcat|link]]|
 ^Repeat annotation|Repeat Masker|Smith-Waterman based identification and optional masking of repeats provided in a repeat database|no|[[https://anaconda.org/bioconda/repeatmasker|bioconda]]|[[http://www.repeatmasker.org/|Link]]| ^Repeat annotation|Repeat Masker|Smith-Waterman based identification and optional masking of repeats provided in a repeat database|no|[[https://anaconda.org/bioconda/repeatmasker|bioconda]]|[[http://www.repeatmasker.org/|Link]]|
 ^Genome visualization|JBrowse Desktop|Desktop version of JBrowse that does not need any web server configuration|yes|[[https://jbrowse.org/blog/|manually]]|[[http://gmod.org/wiki/JBrowse_Desktop|Link]]| ^Genome visualization|JBrowse Desktop|Desktop version of JBrowse that does not need any web server configuration|yes|[[https://jbrowse.org/blog/|manually]]|[[http://gmod.org/wiki/JBrowse_Desktop|Link]]|
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 ^Ortholog search|InParanoid|Pairwise ortholog search tool |no |[[http://software.sbc.su.se/cgi-bin/request.cgi?project=inparanoid|manually]] |[[http://software.sbc.su.se/cgi-bin/request.cgi?project=inparanoid|Link]] | ^Ortholog search|InParanoid|Pairwise ortholog search tool |no |[[http://software.sbc.su.se/cgi-bin/request.cgi?project=inparanoid|manually]] |[[http://software.sbc.su.se/cgi-bin/request.cgi?project=inparanoid|Link]] |
 | |OMA |Ortholog matrix project | no |[[https://omabrowser.org/standalone/#downloads|manually]] |[[https://omabrowser.org/standalone/|Link]] |  | |OMA |Ortholog matrix project | no |[[https://omabrowser.org/standalone/#downloads|manually]] |[[https://omabrowser.org/standalone/|Link]] | 
-| |fDOG |Targeted ortholog search tool |no |[[https://github.com/BIONF/fDOG|manually]] |[[https://github.com/BIONF/fDOG|Link]] | +| |fDOG |Targeted ortholog search tool |no |[[https://github.com/BIONF/fDOG|pip]] |[[https://github.com/BIONF/fDOG|Link]] | 
-^ Phylogenetic Profiling|PhyloProfile |A browser based tool for visualizing and exploring phylogenetic profiles |yes |[[https://github.com/BIONF/PhyloProfile|manually]] |[[https://github.com/BIONF/PhyloProfile|Link]] |+^ Phylogenetic Profiling|PhyloProfile |A browser based tool for visualizing and exploring phylogenetic profiles |yes |[[https://github.com/BIONF/PhyloProfile|Bioconductor]] |[[https://github.com/BIONF/PhyloProfile|Link]] |
 ^Phylogeny reconstruction|RAxML |Phylogenetics - Randomized Axelerated Maximum Likelihood |no |[[https://anaconda.org/bioconda/raxml|bioconda]] |[[http://sco.h-its.org/exelixis/web/software/raxml/index.html|Link]] | ^Phylogeny reconstruction|RAxML |Phylogenetics - Randomized Axelerated Maximum Likelihood |no |[[https://anaconda.org/bioconda/raxml|bioconda]] |[[http://sco.h-its.org/exelixis/web/software/raxml/index.html|Link]] |
 | |ProtTest3 |ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand|yes|[[https://github.com/ddarriba/prottest3|manually]]|[[https://github.com/ddarriba/prottest3|Link]]| | |ProtTest3 |ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand|yes|[[https://github.com/ddarriba/prottest3|manually]]|[[https://github.com/ddarriba/prottest3|Link]]|
 ^Tree visualization|FigTree|Graphical viewer of phylogenetic trees|yes|[[https://github.com/rambaut/figtree/|manually]]|[[https://github.com/rambaut/figtree/|Link]]| ^Tree visualization|FigTree|Graphical viewer of phylogenetic trees|yes|[[https://github.com/rambaut/figtree/|manually]]|[[https://github.com/rambaut/figtree/|Link]]|
 | |iTOL|Interactive software for the visualisation and annotation of phylogenetic trees|yes|[[https://itol.embl.de|Web tool]]|[[https://itol.embl.de|Link]]| | |iTOL|Interactive software for the visualisation and annotation of phylogenetic trees|yes|[[https://itol.embl.de|Web tool]]|[[https://itol.embl.de|Link]]|
 +| |matt|Interactive tree visualisation, modification and topology testing|yes|[[https://github.com/BIONF/matt#installation |pip]]|[[https://github.com/BIONF/matt|Link]]|
 ^Sequence alignment|Muscle|Multiple sequence alignment|no|[[https://anaconda.org/bioconda/muscle|bioconda]]|[[https://www.drive5.com/muscle/manual/index.html|Link]]| ^Sequence alignment|Muscle|Multiple sequence alignment|no|[[https://anaconda.org/bioconda/muscle|bioconda]]|[[https://www.drive5.com/muscle/manual/index.html|Link]]|
 | | | | | | | | | | | |
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 ==== JBrowse ==== ==== JBrowse ====
-We will use the [[http://gmod.org/wiki/JBrowse_Desktop|desktop version of JBrowse]] for our course. Download the version that matches your operating system from the [[https://jbrowse.org/blog/|JBrowse web sites]] and follow the installation guidelines provided with the software.+In case you want to use the [[http://gmod.org/wiki/JBrowse_Desktop|desktop version of JBrowse]] for your work, download the version that matches your operating system from the [[https://jbrowse.org/blog/|JBrowse web sites]] and follow the installation guidelines provided with the software.
  
 ===== Databases ===== ===== Databases =====
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   * Uniprot - [[http://www.uniprot.org/|http://www.uniprot.org/]]   * Uniprot - [[http://www.uniprot.org/|http://www.uniprot.org/]]
   * PFAM - [[http://pfam.xfam.org/|http://pfam.xfam.org/]]   * PFAM - [[http://pfam.xfam.org/|http://pfam.xfam.org/]]
 +  * InterPro - [[https://www.ebi.ac.uk/interpro/]]
   * HMMER - [[http://hmmer.org/|http://hmmer.org/]]   * HMMER - [[http://hmmer.org/|http://hmmer.org/]]
-  * gNOME - [[http://ghubs.izn-ffm.intern:5000/g-nom/assemblies/list]] :!: This is an ongoing project, and we will be working with an alpha version of this web tool. The URL is reachable only from within our network. +  * gNOME - [[http://ghubs.izn-ffm.intern:5000/g-nom/assemblies/list]] :!: This is an ongoing project, and we will be working with an alpha version of this web tool. The %%URL%% is reachable only from within our network.
  
 +<WRAP tabs>
 +   * [[ecoevo_molevol:course_introduction|Back to EcoEvo course]]
 +   * [[pbioc_basics:start|Back to PBioC course]]
 +   * [[digikomp_bio:course_introduction|Back to DigiKomp course]]
 +   * [[mbw_bioinf:mastermbw| Back to MBW course]]
 +</WRAP>