| 1 |
mlst |
https://github.com/tseemann/mlst |
|
| 2 |
t6ss_finder |
|
|
| 3 |
parsnp |
https://github.com/marbl/parsnp |
1.2、1.7.4 |
| 4 |
harvesttools |
|
1.1.2 |
| 5 |
grapetree |
|
|
| 6 |
usher |
https://github.com/bpt26/usher_wiki |
0.6.2 |
| 7 |
FastTree |
http://www.microbesonline.org/fasttree/ |
2.1.11 |
| 8 |
iqtree |
http://www.iqtree.org/ |
|
| 9 |
RAxML |
|
|
| 10 |
kmerfinder |
https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/ |
|
| 11 |
datasets |
https://github.com/ncbi/datasets |
|
| 12 |
isescan |
https://github.com/xiezhq/ISEScan |
|
| 13 |
snakemake |
https://snakemake.github.io/ |
|
| 14 |
ClermonTyping |
https://github.com/A-BN/ClermonTyping |
|
| 15 |
EzClermont |
https://github.com/nickp60/ezclermont |
|
| 16 |
FimTyper |
https://bitbucket.org/genomicepidemiology/fimtyper |
|
| 17 |
vcftools |
https://vcftools.github.io/ |
0.1.16 |
| 18 |
blast |
https://blast.ncbi.nlm.nih.gov/ |
|
| 19 |
prodigal |
|
|
| 20 |
kingfisher |
https://github.com/wwood/kingfisher-download |
3.0 |
| 21 |
ascp |
https://ak-delivery04-mul.dhe.ibm.com/sar/CMA/OSA/09cne/0/ |
|
| 22 |
Abyss |
https://github.com/bcgsc/abyss |
|
| 23 |
chewBBACA |
https://github.com/B-UMMI/chewBBACA |
|
| 24 |
diamond |
|
|
| 25 |
Rfam |
https://rfam.org/ |
|
| 26 |
infernal |
http://eddylab.org/infernal/ |
|
| 27 |
ECTyper |
|
|
| 28 |
GenoTyphi |
|
|
| 29 |
pubMLST |
https://pubmlst.org/ |
|
| 30 |
BIGSdb |
https://github.com/kjolley/BIGSdb. |
|
| 31 |
EnteroBase |
https://enterobase.warwick.ac.uk/ |
|
| 32 |
NCBI |
https://www.ncbi.nlm.nih.gov/ |
|
| 33 |
SeqSero2 |
https://github.com/denglab/SeqSero2 |
|
| 34 |
SPIFinder |
https://cge.cbs.dtu.dk/services/SPIFinder/ |
|
| 35 |
Bcereus |
|
|
| 36 |
SecReT6 |
https://bioinfo-mml.sjtu.edu.cn/SecReT6/index.php |
|
| 37 |
tblg |
https://github.com/dbespiatykh/tblg |
|
| 38 |
GPSC |
https://www.pneumogen.net/gps/#/ |
|
| 39 |
tvBOT |
https://www.chiplot.online/tvbot.html |
|
| 40 |
chiplot |
https://www.chiplot.online/ |
|
| 41 |
antismash |
https://antismash.secondarymetabolites.org/#!/start |
|
| 42 |
RepeatMasker |
https://www.repeatmasker.org/ |
|
| 43 |
cazy |
http://www.cazy.org/ |
|
| 44 |
tcdb |
https://www.tcdb.org/ |
|
| 45 |
pfam |
http://pfam.xfam.org/ |
|
| 46 |
uniprot |
https://www.uniprot.org/ |
|
| 47 |
phi |
http://www.phi-base.org/ |
|
| 48 |
amrfinder |
https://github.com/ncbi/amr/wiki |
|
| 49 |
VFDB |
http://www.mgc.ac.cn/VFs/main.htm |
|
| 50 |
EVA-13-935-s004.py |
|
|
| 51 |
RGI |
https://github.com/arpcard/rgi |
|
| 52 |
CARD |
https://card.mcmaster.ca/ |
|
| 53 |
phispy |
https://github.com/linsalrob/PhiSpy |
|
| 54 |
CroTrait |
https://github.com/happywlu/CroTrait |
|
| 55 |
kaptive |
https://github.com/klebgenomics/Kaptive |
|
| 56 |
IslandPath-DIMOB |
https://github.com/brinkmanlab/islandpath |
|
Softwares