| Trimmomatic |
v0.33/v0.36 |
Cleaning and trimming of Illumina reads |
http://www.usadellab.org/cms/?page=trimmomatic |
| BWA |
v0.7 |
Alignment of reads to reference sequence |
https://github.com/lh3/bwa |
| Picard |
v2.16 |
Manipulation of high-throughput sequence data |
https://broadinstitute.github.io/picard |
| SAMtools |
v1.3/v1.9 |
Manipulation of high-throughput sequence data |
https://github.com/samtools/samtools |
| BCFtools |
v1.4.1 |
Manipulation of high-throughput sequence data |
https://github.com/samtools/bcftools |
| VCFtools |
v0.1.12b/v0.1.13 |
Manipulation of high-throughput sequence data |
https://github.com/samtools/bcftools |
| seqtk |
v1.2 |
Manipulation of sequences in fasta and fastq format |
https://github.com/lh3/seqtk |
| BBMap |
v37.47 |
Merging overlapping reads into a single read |
https://github.com/BioInfoTools/BBMap |
| SPAdes |
v3.9.1 |
Genome assembly |
https://github.com/ablab/spades |
| Mauve |
v2015-02-13 |
Genome alignment |
http://darlinglab.org/mauve/mauve.html |
| BEDtools |
v2.26.0 |
A suite of command line tools for working with genome data |
https://github.com/arq5x/bedtools2 |
| RaxML |
v8.2.9/v8.2.12 |
Analysis of phylogenies |
https://github.com/stamatak/standard-RAxML |
| STRUCTURE |
v2.3.4 |
Analysis of population genetic data using multilocus data |
https://web.stanford.edu/group/pritchardlab/structure.html |
| SplitsTree |
v4.14.5 |
Computation of phylogenetic networks |
http://www.splitstree.org |
| TreeCollapseCL |
v4 |
Manipulation of phylogenetic trees |
http://emmahodcroft.com/TreeCollapseCL.html |
| ANGSD |
v0.924 |
Analysis of next generation sequencing data |
https://github.com/ANGSD/angsd |
| circos |
v0.69-6 |
Circular visualization of the data |
http://circos.ca |
| Plink |
v1.9 |
Manipulation of high-thoughput sequence data |
http://pngu.mgh.harvard.edu/purcell/plink |
| Blast2GO Basic |
v5.2 |
Functional annotation of genomic datasets |
https://www.blast2go.com |
| EffectorP |
v1.0 |
Prediction of fungal effector proteins from secretomes |
http://effectorp.csiro.au |
| SnIPRE |
downloaded 2019-01 |
Inference of selection in large gene datasets |
https://bustamantelab.stanford.edu/lab-developed-software |
| D-Genies |
v1.2.0 |
Display of dot plots of genome alignments |
http://dgenies.toulouse.inra.fr |
| NUCmer |
v3 |
Genome alignment |
http://mummer.sourceforge.net |
| DIAMOND |
v0.9.22 |
Local sequence alignment |
https://github.com/bbuchfink/diamond |
| mstatspop |
v0.1 |
Analysis of population genomic data |
https://github.com/CRAGENOMICA/mstatspop |
| Twisst |
downloaded 2018-02 |
Topology weighting |
https://github.com/simonhmartin/twisst |