146 project(s) on this page
Project | Selected | Spr | Newest | Outdated | Ignored |
---|---|---|---|---|---|
andi | 0.13 | 7 | 0.145 | 0.13 0.12 0.9.6.1 | 0.14.3 |
aragorn | 1.2.38 | 6 | 1.2.415 | 1.2.382 1.2.36 | |
arcs | 1.2.1 | 2 | 1.2.5 | ||
artemis-genome-viewer | 17.0.1 | 4 | 18.2.02 | 18.1.0 17.0.1.11 17.0.1 16.0.17 16.0.0 | |
bali-phy | 3.6.0 | 4 | 4.0 | 4.0~beta16 4.0-beta10 4.0~beta2 3.6.13 3.6.0 3.4.1 3.4 | |
bandage | 0.8.1 | 5 | 0.9.03 | 0.8.12 | |
bbtools∗ | 38.87 | 2 | 39.28 | 1.9 | |
bcalm∗ | 2.2.2 | 3 | 2.2.3 | 2.2.1 | 2.2.0.r49.g890ea4a |
beast2 | 2.6.3 | 5 | 2.7.72 | 2.7.6 2.7.4 2.7.3 2.6.6 2.6.3 2.6.0 2.5.1 2.4.7 2.4.4 | |
bfc | r181 | 5 | 1.12.0 | 1.0.1 0.2 g20150417 | |
bifrost | 1.0.5 | 6 | 1.20.22 | 1.3.52 1.3.1 | |
blat | 36 | 5 | 37 | 34 3.2.24 3.2.1 3.1.1 3.0.7 3.0.2 3 2.7.6 2.6.2 | |
bmdca | 0.8.12 | 2 | 0.8.13 | ||
bowtie∗ | 1.3.0 | 12 | 1.3.111 | 1.3.03 1.2.32 1.2.2 1.1.2 1.0.0 0.12.7 | |
bracken | 2.6.0 | 3 | 3.1 | 2.9 | |
breseq | 0.35.4 | 2 | 0.39.0 | 0.38.1 | HEAD |
busco | 5.0.0 | 4 | 5.5.0 | 5.4.4 5.4.3 5.2.2 5.0.0 | 3.0.0 |
bwa-mem2 | 2.0 | 5 | 2.2.13 | r183.d43752d 2023-03-18 | |
canu | 1.9 | 6 | 2.3 | 2.24 2.0 1.9 1.8 1.6 | 2.2.r162.gc61ebbb7a |
cap3 | 2015-02-11 | 3 | 20091029 | 2015-02-11 | |
centrifuge | 1.0.3 | 6 | 1.0.4.23 | 1.0.4.1 1.0.4 1.0.3 1.0.3~beta | |
circlator | 1.5.5 | 2 | 1.5.6 | 1.5.5 | |
clonalframeml | 1.12 | 3 | 1.132 | 1.12 1.11 | |
cutadapt∗ | 3.3 | 5 | 5.1 | 4.9 4.0 1.14 | |
delly∗ | 0.8.5 | 5 | 1.3.32 | 1.3.1 1.2.6 1.1.82 1.1.62 0.9.1 0.8.7 0.8.3 0.8.2 0.8.1 | |
dida∗ | 1.0.1 | 3 | 6.0.30 | 6.0.6.0 6.0.5.0 6.0.4.0 6.0.3.0 6.0.2.0 6.0.1.0 6.0.0.1 6.0.0.0 5.5.0.0 5.4.0.0 5.3.0.2 5.2.0.0 5.1.0.0 5.0.6.0 5.0.5.0 5.0.4.0 3.7.8.8 1.0.4 | 1.0.4.r5.gbcb26e5 6.3.2.0 6.3.1.2 6.3.1.1 6.3.1.0 6.3.0.2 6.3.0.1 6.3.0.0 6.2.4.5 6.2.4.0 6.2.3.0 6.2.2.0 6.2.1.0 6.2.0.0 6.1.6.0 6.1.5.0 6.1.4.0 6.1.3.0 6.1.2.0 6.1.1.0 6.1.0.0 |
dssp | 3.1.4 | 10 | 4.5.32 | 4.5.02 4.4.112 4.4.103 4.4.7 4.4.5 4.2.2.1 4.2.2 4.0.5 4.0.4 4.0.0 3.1.43 3.0.02 2.2.13 | |
dwgsim | 0.1.12 | 2 | 0.1.14 | 0.1.13 0.1.12 0.1.11 | |
e-mem | 1.0.1 | 4 | 28oct2015 | 1.0.12 | |
easel | 0.46 | 2 | 0.49 | ||
exabayes | 1.5 | 3 | 1.5.12 | ||
falco-fastqc | 0.2.4 | 3 | 1.2.3 | 1.2.1 | |
fasta | 36.3.8h | 7 | 36.3.8i2 | 36.3.8h_2020-05-04 36.3.8h.2020-02-11 36.3.8h2 36.3.8g2 36.3.8d 36.3.8 21.1.1 | 36.3.8i.2023.09t 36.3.8i.14-Nov-2020 |
fastani | 1.32 | 6 | 1.344 | 1.33 | |
fastp | 0.20.1 | 10 | 1.0.12 | 0.26.02 0.24.12 0.24.03 0.23.44 0.23.3 0.23.23 0.22.0 0.20.1 0.20.0 0.19.6 | |
filtlong | 0.2.0 | 5 | 0.2.13 | 0.2.0-1.d1bb46d 0.2.0 | |
finch-rs∗ | 0.3.0 | 2 | 0.6.2 | ||
flye∗ | 2.8.3 | 3 | 2.9.62 | 2.9.52 2.9.42 2.9.3 2.9.1 | HEAD |
freebayes | 1.3.2 | 8 | 1.3.10 | 1.3.94 1.3.7 1.3.62 1.3.52 1.3.2 1.3.1 1.2.0 1.1.0 | HEAD |
gatk | 4.2.0.0 | 6 | 4.6.2.02 | 4.6.1.03 4.5.0.02 4.4.0.0 4.3.0.0 3.8-1 | |
gemma | 0.98.4 | 5 | 0.98.53 | 0.98.4 0.98.3 0.98.1 | |
gffcompare∗ | 0.12.1 | 5 | 0.12.62 | 0.12.2 0.10.15-1.be56ef4 | |
hmmer | 2.4i | 17 | 3.411 | 3.3.25 3.3 3.2.1 3.1beta2 3.1b2 3.1_beta2 3.1b1 3.02 3 2.4i 2.3.23 | |
infernal | 1.1.3 | 8 | 1.1.55 | 1.1.42 1.1.3 1.1.2 1.1.1 1.1~rc4 1.0.22 | |
iqtree∗ | 1.6.12 | 7 | 3.0.1 | 2.4.0 2.3.6 2.3.4 2.2.2.72 2.2.2.4 2.2.0.4 2.0.7 1.6.122 1.6.9 1.6.1 1.3.11.1 | |
iqtree2∗ | 2.0.7 | 2 | 2.1.3 | ||
iva∗ | 1.0.9 | 2 | 1.0.11 | 1.0.9 | |
ivar | 1.3 | 3 | 1.4.4 | 1.4.3 1.4.22 1.3.1 1.3 | |
jellyfish-k-mer | 2.3.0 | 8 | 2.3.14 | 2.3.04 2.2.10 2.2.8 2.2.4 1.1.122 1.1.11 1.1.10 | |
jmol | 14.31.34 | 15 | 16.3.272 | 16.3.25 16.3.21 16.3.17 16.3.7 16.3.1 16.2.33 16.2.17 16.2.153 16.1.63 16.1.47 16.1.45 16.1.43 16.1.25 16.1.13 16.1.11 16.1.9 14.32.832 14.32.76 14.32.74 14.32.73 14.32.3 14.31.44 14.31.20 14.31.0 14.30.0 14.29.54 14.29.52 14.6.4+2016.11.05 14.2.9_2014.11.23 12.2.32 | |
Project | Selected | Spr | Newest | Outdated | Ignored |
k8 | 0.2.5 | 2 | 1.0 | ||
kaiju-metagenomics | 1.7.4 | 4 | 1.10.1 | 1.9.0 1.6.2 | |
kalign | 3.3 | 6 | 3.4.04 | 3.3.53 3.3.1 3.3 2.03+20110620 2.03 | |
kma | 1.3.6 | 4 | 1.5.1 | 1.5.0 1.4.21 1.4.15 1.4.14 1.4.11 1.3.28 1.3.23 1.3.10 1.2.21 | |
kmc | 3.1.1 | 2 | 3.2.4 | 3.2.1 3.1.1 2.3 | |
kmergenie | 1.7048 | 2 | 1.7051 | ||
kraken2 | 2.1.1 | 6 | 2.14 | 2.1.52 2.1.3 2.1.23 2.1.1 2.0.8~beta | HEAD |
kssd | 1.1 | 2 | 2.21 | 1.1 | |
last | 1133 | 6 | 16393 | 1609 1592 1543 1542 14992 1453 1447 1411 1260 1179 1060 963 921 712 393 | |
lastz | 1.04.03 | 6 | 1.04.522 | 1.04.41 1.04.222 1.04.15 1.04.032 | HEAD |
libbigwig | 0.4.4 | 9 | 0.4.76 | 0.4.6 0.4.43 | 9999 0.4.8 |
libccp4∗ | 6.5.1 | 7 | 8.0.04 | 6.5.12 6.4.6 6.4.5 | r1896 |
libdivsufsort | 2.0.1 | 14 | 2.0.2.1 | 2.0.112 | HEAD 2.0.2.1.20151027 |
libpll | 0.3.2 | 4 | 1.0.11 | 0.3.22 0.3.1 | |
lighter | 1.1.2 | 5 | 1.1.32 | 1.1.23 | 9999 |
lofreq | 2.1.3.1 | 2 | 2.1.5 | ||
maker | 2.31.11 | 2 | 3.01.04 | ||
mapcaller | 0.9.9.39 | 2 | 0.9.9.41 | ||
mash-genome-distance | 2.2.2 | 5 | 2.33 | 2.2.2 2.12 2.0 | |
masurca | 3.4.1 | 3 | 4.1.1 | 4.1.0 4.0.1 | |
mcl∗ | 14-137 | 9 | 22.282 22-282 | 14-1373 14_1372 14.1372 12-135 1.008.09.149 | |
megahit | 1.2.9 | 9 | 1.2.9.20 | 1.2.96 1.1.4 | |
meme-motif-discovery∗ | 5.1.0 | 5 | 5.5.82 | 5.5.7 5.5.42 | |
metaphlan∗ | 1.7.8 | 2 | 4.0.4 | ||
minia∗ | 3.2.1 | 4 | 3.2.6 | 3.2.1+git20200522.4960a99 3.2.1 1.6906 1.6067 | 3.2.1.r12.g5b131b9 |
minigraph | 0.10 | 2 | 0.212 | ||
minimap2∗ | 2.17 | 9 | 2.304 | 2.29 2.285 2.27 2.262 2.243 2.17 2.15 | 2.24.r39.g5e72423 |
mlst | 2.19.0 | 2 | 2.23.0 | ||
mmdb2∗ | 2.0.20 | 6 | 2.0.224 | 2.0.1 | |
mmtf-cpp∗ | 1.0.0 | 16 | 1.1.014 | 1.0.08 | |
mosdepth | 0.3.1 | 4 | 0.3.112 | 0.3.10 0.3.9 0.3.8 0.3.6 0.3.5 0.3.4 0.3.32 0.3.1 | |
mothur | 1.44.3 | 6 | 1.48.3 | 1.48.2 1.48.1 1.48.03 1.47.0 1.44.3 1.42.1 1.39.5 1.36.1 1.31.2 1.27.0 1.41.21 | |
mpboot | 1.1.0 | 2 | 1.2 | ||
mrbayes∗ | 3.2.7 | 9 | 3.2.7a4 | 3.2.75 3.2.6 3.2.2 3.1.2 | HEAD |
mummer∗ | 3.23 | 8 | 4.0.14 | 4.0.0rc1 3.233 3.20 | |
muscle-sequence-alignment∗ | 3.8.1551 | 12 | 5.32 | 5.1.03 3.8.15515 3.8.315 | |
nanofilt | 2.7.1 | 2 | 2.8.0 | 2.6.0 | |
nanopolish | 0.12.0 | 5 | 0.14.03 | 0.13.3 0.13.2 0.11.3 0.11.0 0.9.0 0.4.0 | 9999 0.14.0.r10.g21c75db |
ncbi-blast+∗ | 2.2.31 2.2.26 | 12 | 2.16.06 | 2.14.12 2.14.0 2.13.03 2.12.0 2.11.0 2.9.0 2.8.1 2.6.0 2.2.31 2.2.29 2.2.28 2.2.26 | |
nextflow | 20.07.1 | 5 | 25.04.4 | 25.04.3 24.08.0-edge 24.04.3 22.04.5 | |
nthits | 0.0.1 | 2 | 1.0.2 | ||
paml∗ | 4.9j | 10 | 4.10.92 | 4.10.74 4.10.6 4.9j4 4.9h 4.9g 4.9e 4.8 4.7 | |
parasail | 2.4.2 | 3 | 2.6.22 | 2.6 2.5 2.4.3 | |
parsnp | 1.5.2 | 2 | 2.1.3 | 2.0.6 2.0.3 1.7.4 1.6.2 1.5.4 1.2.1 1.2 | |
percolator | 3.05 | 4 | 3.08 | 3.7.1 3.06.04 3.06.01 3.05 3.02.00 | 3.07 |
phylip | 3.697 | 9 | 3.6982 | 3.6975 3.696 3.695 3.69 | |
phyml∗ | 3.3.20200621 | 9 | 3.3.202204086 | 3.3.20211231 3.3.20200621 3.3.20190909 3.3.20180621 3.3.20170530 3.2.0 2.4.5 | 201204122 3.3.20250515 |
phyx | 1.01 | 3 | 1.3.22 | 1.3.1 1.3 1.01 0.999 | |
pilon | 1.23 | 4 | 1.242 | 1.23 1.22 | |
pirate | 1.0.4 | 2 | 5.9.0 | ||
Project | Selected | Spr | Newest | Outdated | Ignored |
plink∗ | 1.90b5 | 10 | 1.90.b6.17 1.075 | 1.90~b6.16-200217 1.90~b6.6-181012 1.90~b5.2-180109 1.90~b3.31-160203 1.90b3 1.9-beta6.27 | 1.9.r108.ga09b4443 1.90_pre140514 1.90~b7.7-241022 1.90~b7.2-231211 1.90~b6.26-220402 1.90~b6.21-201019 |
portcullis | 1.1.0 | 2 | 1.2.3 | ||
pplacer | 1.1.alpha17 | 3 | 1.1~alpha19 1.1.alpha19 | ||
pymol | 2.4.0 | 19 | 3.1.07 | 3.0.05 2.5.7 2.5.5 2.5.08 2.4.02 2.3.03 2.2.02 1.8.6.0 1.8.4.0 1.7.2.1 1.7.0.0 0.1.0 | r5647.071998658 HEAD 20250617-7e6dafa7 3.1.6.1 3.1.6 3.1.5.1 3.1.4.1 3.1.4 3.1.3.1 |
python:matplotlib∗ | 3.3.4 | 40 | 3.10.319 | 3.10.18 3.10.02 3.9.42 3.9.32 3.9.2 3.9.12 3.9.0 3.8.44 3.8.35 3.8.22 3.8.04 3.7.4 3.7.3 3.7.23 3.7.14 3.7.0 3.6.33 3.6.23 3.6.0 3.5.3 3.5.2 3.5.14 3.4.32 3.4.22 3.3.4 3.3.32 3.2.1 3.1.2 3.0.32 3.0.2 2.2.54 2.2.43 2.2.3 2.1.1 1.5.12 1.3.12 1.2.02 0.99.1.22 | r49602.5e34777719 |
quast | 5.0.2 | 2 | 5.3.0 | 5.0.2 | |
quip | 1.1.8 | 2 | 8.92.0 | ||
racon | 1.4.13 | 5 | 1.5.03 | 1.4.20 1.4.10 1.4.3 1.3.2 | 1.5.0.r0.ga2cfcac |
raptor∗ | 1.1.0 | 40 | 2.0.1630 | 2.0.1520 2.0.14.1 2.0.14 2.0.13 2.0.92 2.0.3 2.0.2 2.0.0 1.4.218 1.4.20 1.4.19 1.4.18 0.8.0 | 2022-06-06 |
rasusa∗ | 0.3.0 | 1 | 2.1.0 | HEAD | |
raxml∗ | 8.2.12 | 9 | 8.2.134 | 8.2.126 8.2.11 8.2.4 7.2.8 | |
repeatmasker∗ | 4.0.7 | 3 | 4.1.52 | ||
rna-star | 2.7.5c | 11 | 2.7.11b5 | 2.7.11.a 2.7.10b3 2.7.10a3 2.7.8a2 2.7.3a2 2.7.2a 2.7.1a 2.7.0a 2.5.4b 2.5.0a | |
rtg-tools | 3.11 | 3 | 3.13 | 3.12.12 | |
ruby:rails∗ | 1.5.1▲ | 22 | 8.0.27 | 8.0.12 7.2.2.15 7.2.2 7.1.5.14 7.1.5 7.1.4.2 7.1.3.4 7.1.2▲ 7.0.8.7▲3 7.0.8.6▲ 7.0.8▲ 7.0.7.2▲ 7.0.7▲ 7.0.5.1▲ 7.0.4.3▲3 7.0.4▲ 7.0.2.3▲ 6.1.7.103 6.1.7.3▲ 6.1.7.1▲ 6.1.4.1▲2 6.0.6.1▲ 6.0.3.7▲ 6.0.2.2▲ 5.2.8.1▲ 5.2.4.4▲ 5.2.4.3▲ 5.2.4.1▲ 5.2.3▲2 5.2.2.1▲ 5.2.1▲ 5.1.7▲ 5.1.6▲ 5.1.4▲ 5.0.7.2▲ 4.2.11.3▲ 4.2.10▲ 4.2.6▲ 4.2.5.1▲ 4.0.2▲ 3.2.19▲ 3.2.18▲ 3.2.16▲ 3.2.13+1▲ 3.0.5▲ 2.3.5▲ 1.5.1▲ 1.1.6▲ | |
salmon | 1.3.0 | 8 | 1.10.33 | 1.10.22 1.10.12 1.4.0 1.2.2 0.12.0 0.7.2 | |
sambamba | 0.7.1 | 6 | 1.0.14 | 1.0.0 1.0 0.8.24 0.8.0 0.6.7 0.6.6 | |
sdsl-lite∗ | 2.1.1 | 8 | 3.0.3 | 3.0.2 3.0.1 2.3.1 2.1.1.137 2.1.14 2.0.3 v2.1.1.r132.gddb0fbbc | |
sepp | 4.3.10 | 3 | 4.5.5 | 4.5.1+really4.5.1 4.5.1 4.3.10 | |
seqan | 3.0.2 2.4.0 | 12 | 3.4.0~rc3 3.4.0-rc3 3.3.06 | 3.4.0-rc1 3.3.0-rc2 3.2.02 3.1.03 3.0.32 3.0.2 3.0.1 2.5.1 2.5.0 2.5.0~rc3 2.4.08 2.3.2 1.4.24 1.4.1 1.3.12 | 3.0.0.r465.g4cdd84b2 |
seqkit | 0.15.0 | 7 | 2.10.05 | 2.9.02 2.8.22 2.5.13 2.4.0 2.3.12 2.1.0 0.15.0 | HEAD |
slim-simulator∗ | 3.5 | 3 | 5.0 | 5.0.r0.gacf0f088 | |
snap-gene-prediction∗ | 2013-11-29 | 2 | 20131129 | ||
snpeff | 4.3t | 8 | 5.2 | 5.2.f 5.2.b 5.1+d 5.12 4.3t3 | 2017-11-24 |
sortmerna | 2.1 | 5 | 4.3.72 | 4.3.6 4.3.4 4.2.0 2.1 2.0 | 2017-07-13 |
stacks | 2.41 | 10 | 2.685 | 2.67 2.662 2.65 2.622 2.603 2.55 2.53 2.41 2.2 2.1 2.0Beta8c 1.35 1.9.14 1.9.13 1.9.12 1.9.10 1.9.7 1.9.6 1.9.5 1.9.4 1.9.3 1.9.2 1.9.1 1.9.0 1.8.3 1.8.2 1.8.1 1.8.0 1.7.6 1.7.5 1.7.4 1.7.3 1.7.1 1.7.0 1.6.3 1.6.2 1.6.1 1.5.7 1.5.6 1.5.5 1.5.4 1.5.3 1.5.2 1.5.1 1.4.7 1.4.6 1.4.5 | |
staden-io-lib∗ | 1.14.13 | 5 | 1.15.03 | 1.14.15 1.14.14 1.14.13 1.14.11 1.14.9 1.14.8 1.14.6 1.13.5 1.12.4 | |
stringtie | 2.1.4 | 10 | 3.0.1 | 3.0.02 2.2.12 2.2.0 2.1.5 2.1.4 2.1.13 1.3.6 | HEAD |
subread | 2.0.1 | 9 | 2.1.12 | 2.1.0 2.0.82 2.0.7 2.0.63 2.0.34 2.0.1 2.0.0 1.6.3 1.6.0 1.5.0-p1 | |
sumaclust∗ | 1.0.31 | 4 | 1.0.36 | 1.0.35 1.0.34 1.0.31 1.0.20 1.0.10 | |
taxonkit | 0.7.2 | 3 | 0.14.2 | 0.19.0 | |
tmalign∗ | 20190822 | 2 | 20220412 | ||
transdecoder | 5.5.0 | 5 | 5.7.13 | 5.5.0 5.0.1 2.0.1 | |
trf-tandem-repeats-finder∗ | 4.09 | 5 | 4.09.13 | 4.09 4.04 | |
trimal | 1.4.1 | 5 | 1.5.04 | 1.4.12 | HEAD |
trinityrnaseq | 2.11.0 | 6 | 2.15.2 | 2.15.12 2.15.1.FULL 2.13.23 2.11.0 2.6.6 2.5.1 | |
trnascan-se | 2.0.4 | 6 | 2.0.123 | 2.0.11 2.0.10 2.0.9 2.0.7 2.0.5 2.0.0 1.31 1.3.1 | |
ucsc-genome-browser | 401 | 4 | 483 | 468 446 404 260 | |
unicycler∗ | 0.4.7 | 3 | 0.5.1 | 0.5.02 0.4.8 0.4.7 | |
unikmer | 0.11.0 | 3 | 0.20.02 | 0.19.1 0.18.8 | |
varscan | 2.4.3 | 5 | 2.4.6 | 2.4.42 2.4.3 2.4.2 2.3.9 | |
vcflib∗ | 1.0.1 | 5 | 1.0.14 | 1.0.13 1.0.12 1.0.3 | 1.0.3.r330.ga36dbe9 |
viennarna∗ | 2.4.17 | 7 | 2.7.04 | 2.6.4 2.5.1 2.4.18 2.4.17 | |
vt | 0.5772 | 5 | 0.577213 | 9999 | |
wiggletools | 1.2.10 | 3 | 1.2.112 | ||
wish | 1.0 | 2 | 1.3 | 1.3.r7905f84 |
Legend: