| Software, algorithm |
ABRicate |
https://github.com/tseemann/abricate
|
RRID:SCR_021093
|
|
| Software, algorithm |
ACT: Artemis Comparison Tool |
http://www.sanger.ac.uk/resources/software/act/
|
RRID:SCR_004507
|
|
| Software, algorithm |
BactDating |
https://github.com/xavierdidelot/BactDating
|
RRID:SCR_021092
|
|
| Software, algorithm |
BEAST |
http://beast.bio.ed.ac.uk/
|
RRID:SCR_010228
|
|
| Software, algorithm |
Clustal Omega |
http://www.ebi.ac.uk/Tools/msa/clustalo/
|
RRID:SCR_001591
|
|
| Software, algorithm |
Easyfig |
http://easyfig.sourceforge.net/
|
RRID:SCR_013169
|
|
| Software, algorithm |
FastANI |
https://github.com/ParBLiSS/FastANI
|
RRID:SCR_021091
|
|
| Software, algorithm |
Geneious |
http://www.geneious.com/
|
RRID:SCR_010519
|
|
| Software, algorithm |
Gubbins |
https://sanger-pathogens.github.io/gubbins/
|
RRID:SCR_016131
|
|
| Software, algorithm |
iToL |
https://itol.embl.de/
|
RRID:SCR_018174
|
|
| Other |
KEGG |
http://www.kegg.jp/
|
RRID:SCR_012773
|
Online database |
| Software, algorithm |
Kraken2 |
http://www.ebi.ac.uk/research/enright/software/kraken
|
RRID:SCR_005484
|
|
| Software, algorithm |
MAFFT |
http://mafft.cbrc.jp/alignment/server/
|
RRID:SCR_011811
|
|
| Software, algorithm |
MEGA |
http://megasoftware.net/
|
RRID:SCR_000667
|
|
| Software, algorithm |
MUSCLE |
http://www.ebi.ac.uk/Tools/msa/muscle/
|
RRID:SCR_011812
|
|
| Other |
NCBI RefSeq |
https://www.ncbi.nlm.nih.gov/refseq/
|
RRID:SCR_008420
|
Online database |
| Other |
NCBI Sequence Read Archive |
http://www.ncbi.nlm.nih.gov/sra
|
RRID:SCR_004891
|
Online database |
| Software, algorithm |
Panaroo |
https://github.com/gtonkinhill/panaroo
|
RRID:SCR_021090
|
|
| Software, algorithm |
PanGP |
https://pangp.zhaopage.com/
|
RRID:SCR_021089
|
|
| Software, algorithm |
Phandango |
http://phandango.net/
|
RRID:SCR_015243
|
|
| Software, algorithm |
Prokka |
http://www.vicbioinformatics.com/software.prokka.shtml
|
RRID:SCR_014732
|
|
| Other |
PubMLST |
http://pubmlst.org/
|
RRID:SCR_012955
|
Online database |
| Software, algorithm |
pyani |
https://pypi.org/project/pyani/
|
RRID:SCR_021088
|
|
| Software, algorithm |
QUAST |
http://bioinf.spbau.ru/quast
|
RRID:SCR_001228
|
|
| Software, algorithm |
RAxML |
https://github.com/stamatak/standard-RAxML
|
RRID:SCR_006086
|
|
| Software, algorithm |
Roary |
https://sanger-pathogens.github.io/Roary/
|
RRID:SCR_018172
|
|
| Software, algorithm |
Scoary |
https://github.com/AdmiralenOla/Scoary
|
RRID:SCR_021087
|
|
| Software, algorithm |
SPAdes |
http://bioinf.spbau.ru/spades/
|
RRID:SCR_000131
|
|
| Software, algorithm |
SPSS |
https://www.ibm.com/products/spss-statistics
|
RRID:SCR_019096
|
|
| Software, algorithm |
SRST2 |
https://github.com/katholt/srst2
|
RRID:SCR_015870
|
|
| Software, algorithm |
TrimGalore |
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
RRID:SCR_011847
|
|
