200 project(s) on this page
Project | Selected | Spr | Newest | Outdated | Ignored |
---|---|---|---|---|---|
abacas | 1.3.1 | 4 | 1.3.13 | ||
abricate | 1.0.1 | 1 | 1.0.1 | HEAD | |
abyss-explorer | 2.1.0 | 1 | |||
adam∗ | 0.34.0 | 2 | 1.1.1 | ||
ale-assemby-likelihood-estimator | 0.0.20180904 | 1 | |||
andi | 0.13 | 4 | 0.143 | 0.13 0.12 0.9.6.1 | |
any2fasta | 0.4.2 | 4 | 0.4.23 | ||
apbspdb2pqr∗ | 1.5 | 1 | |||
aragorn | 1.2.38 | 5 | 1.2.414 | 1.2.382 1.2.36 | |
arcs | 1.2.1 | 2 | 1.2.2 | ||
arks | 1.0.4 | 1 | |||
art-biostatistics | 20160605 | 1 | |||
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 | |
ascp∗ | 3.7.7 | 1 | |||
astral-species-tree | 5.7.1 | 3 | 5.7.12 | ||
bali-phy | 3.6.0 | 4 | 4.0~beta2 3.6.13 | 3.6.0 3.4.1 3.4 | 4.0-beta6 |
bam2fastx | 1.3.0 | 1 | |||
bamm-bayesian | 2.5.0 | 3 | 2.5.02 | ||
bandage | 0.8.1 | 5 | 0.9.03 | 0.8.12 | |
barrnap | 0.9 | 5 | 0.94 | 0.8 0.7 | 0.9+git20180825.2.acf3198 |
bazam | 1.0.1 | 1 | |||
bbtools∗ | 38.87 | 2 | 39.01 | 1.9 | |
bcalm∗ | 2.2.2 | 3 | 2.2.3 | 2.2.1 | 2.2.0.r49.g890ea4a |
beast2 | 2.6.3 | 5 | 2.7.53 | 2.7.4 2.7.3 2.6.7+git20220420.1.426c992 2.6.6 2.6.3 2.6.0 2.5.1 2.4.7 2.4.4 | |
berokka | 0.2.3 | 1 | |||
bfc | r181 | 5 | 1.12.0 | 1.0.1 0.2 g20150417 | |
bifrost | 1.0.5 | 3 | 1.2.1 | 1.0.5 | |
biobloomtools | 2.3.3 | 1 | |||
biomake | 0.1.5 | 1 | |||
bioperl∗ | 1.007002 | 6 | 1.7.83 | 1.7.73 1.7.2 1.6.924 1.6.923 1.6.9 | HEAD 1.7.8+git20220912.1.4c9acbe |
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 | ||
bodr | 10 | 14 | 1011 | 9 8 | |
bonsai-taxonomic-analysis | 0.3 | 1 | |||
bowtie∗ | 1.3.0 | 12 | 1.3.110 | 1.3.04 1.2.33 1.2.2 1.1.2 1.0.1 1.0.0 0.12.7 | 1.3.1+git20210915.2.86c6d77 |
bracken | 2.6.0 | 3 | 2.9 | 2.8 | |
breseq | 0.35.4 | 2 | 0.38.1 | ||
busco | 5.0.0 | 4 | 5.5.0 | 5.4.7 5.4.4 5.4.3 5.2.2 5.0.0 | 3.0.0 |
bwa-mem2 | 2.0 | 4 | 2.2.1 | 2.0pre1 | r183.d43752d 2023-03-18 |
cannoli∗ | 0.12.0 | 1 | |||
canu | 1.9 | 6 | 2.25 | 2.0 1.9 1.8 1.6 | 2.2.r89.g769108f4b |
cap3 | 2015-02-11 | 3 | 20091029 | 2015-02-11 | |
cd-hit∗ | 4.8.1 | 11 | 4.8.19 | 4.6.8 4.6.6 4.6.4 4.6.1-2012-08-27 | 4.8.1+git20210420.1.4f6720f |
centrifuge | 1.0.3 | 4 | 1.0.42 | 1.0.3 1.0.3~beta | |
circlator | 1.5.5 | 2 | 1.5.6 | 1.5.5 | |
circos∗ | 0.69-9 | 7 | 0.69-92 0.69_9 0.69.9 | 0.69.6 0.69 0.64 0.55 0.49 | |
clipper4coot∗ | 2.1.20180802 | 1 | |||
clonalframeml | 1.12 | 3 | 1.122 | 1.11 | 1.12+git20200925.1.f808bb7 |
clustal-omega∗ | 1.2.4 | 11 | 1.2.49 | 1.2.2 1.2.1 | |
clustalw∗ | 2.1 | 15 | 2.112 | 1.832 | 2.1+lgpl 2.1+lgpl |
Project | Selected | Spr | Newest | Outdated | Ignored |
cluster-picker | 1.2.5 | 1 | |||
consel | 0.20 | 3 | 0.1 | 2011.05.12 | |
crumble | 0.8.3 | 1 | |||
cutadapt∗ | 3.3 | 4 | 4.4 | 4.0 1.14 | |
das-tool | 1.1.2 | 1 | |||
dehomopolymerate | 0.4.0 | 1 | |||
delly∗ | 0.8.5 | 5 | 1.1.63 | 0.9.12 0.8.72 0.8.3 0.8.2 0.8.1 | |
dida | 1.0.1 | 3 | 1.0.80 | 1.0.4 | 1.0.4.r5.gbcb26e5 4.5.7.5 4.5.7.1 4.5.7.0 4.5.6.0 4.5.5.1 4.5.5.0 4.5.1.0 4.5.0.8 4.5.0.6 4.5.0.1 4.5.0.0 4.4.4.6 4.4.4.0 4.4.3.0 4.4.2.0 4.4.1.0 4.4.0.4 4.4.0.2 4.4.0.0 4.3.5.1 4.3.5.0 4.3.4.0 4.3.3.0 4.3.2.0 4.3.1.1 4.3.1.0 4.3.0.0 4.2.9.0 4.2.8.5 4.2.8.1 4.2.8.0 4.2.7.0 4.2.6.0 4.2.5.0 4.2.4.0 4.2.3.0 4.2.2.0 4.2.1.0 4.2.0.0 4.1.5.0 4.1.4.0 4.1.3.6 4.1.3.0 4.1.2.6 4.1.2.0 4.1.1.0 4.0.5.2 3.9.1.0 3.7.8.8 |
discovardenovo∗ | 52488 | 2 | 52488 | ||
disty | 0.1.0 | 2 | 0.1.0 | ||
dsh-bio∗ | 2.0.3 | 1 | |||
dssp∗ | 3.1.4 | 10 | 4.4.3 | 4.4.22 4.4.1 4.3.1 4.2.2.1 4.2.2 4.0.5 4.0.4 4.0.0 3.1.43 3.0.11 3.0.02 2.2.13 | |
dwgsim | 0.1.12 | 3 | 0.1.14 | 0.1.13 0.1.122 0.1.11 | r159.39a1bbb |
e-mem | 1.0.1 | 4 | 28oct2015 | 1.0.12 | |
easel | 0.46 | 1 | |||
edirect∗ | 13.8 | 2 | 13.3.20200128 | ||
elph | 1.0.1 | 5 | 1.0.14 | ||
ema | 0.6.2 | 1 | |||
emboss∗ | 6.6.0 | 15 | 6.6.011 | 6.5.7 6.4.0 6.0.1 | |
epa-ng | 0.3.8 | 1 | |||
exabayes | 1.5 | 3 | 1.5.12 | 1.4.1 | |
exonerate | 2.4.0 | 11 | 2.4.09 | 2.2.02 | |
express-rna-seq | 1.5.3 | 3 | 1.5.32 | ||
falco-fastqc | 0.2.4 | 2 | 1.2.1 | ||
faqcs | 2.10 | 1 | |||
fasta | 36.3.8h | 7 | 36.3.8i.2023.09t | 36.3.8i.14-Nov-2020 36.3.8i.14-Nov-2020+git20221202.1.162df08 36.3.8i 36.3.8h_2020-05-04 36.3.8h.2020-02-11 36.3.8h2 36.3.8g2 36.3.8 21.1.1 | |
fastani | 1.32 | 5 | 1.343 | 1.33+git20220702.1.d776e34 1.33 | |
fastp | 0.20.1 | 9 | 0.23.47 | 0.23.3 0.23.2+git20220519.1.1bc2c53 0.23.23 0.23.1 0.22.0 0.20.1 0.20.0 0.19.6 | |
fastq-pair | 1.0 | 3 | 1.02 | 1.0+git20210411.2.313b136 | |
fasttree | 2.1.11 | 8 | 2.1.115 | 2.1.103 2.1.9 2.1.8 2.1.7 | |
fastuniq | 1.1 | 1 | |||
fermi-lite | 0.1 | 3 | 0.1 | 0.1.r13.g85f159e | 0.1+git20221215.85f159e 0.1+git20190320.b499514 |
figtree | 1.4.4 | 7 | 1.4.45 | 1.4.3 1.4.2 1.4 | 1.4.4.14 |
filtlong | 0.2.0 | 5 | 0.2.13 | 0.2.0-1.d1bb46d 0.2.0 | 0.2.1+git20210730.1.c56f02b |
finch-rs∗ | 0.3.0 | 2 | 0.6.0 | ||
flash-seq∗ | 1.2.11 | 5 | 1.2.114 | ||
flowcraft | 1.4.1 | 1 | |||
flye∗ | 2.8.3 | 2 | 2.9.2 | 2.9.1 | |
fraggenescan | 1.31 | 2 | 1.31 | ||
freebayes | 1.3.2 | 8 | 1.3.73 | 1.3.64 1.3.52 1.3.2 1.3.1 1.2.0 1.1.0 | HEAD |
fwdpp | 0.8.1 | 1 | |||
gappa-phylogenetic-analysis | 0.6.1 | 1 | |||
gatk | 4.2.0.0 | 6 | 4.4.0.04 | 4.3.0.0 4.0.6.0 3.8-1 | |
gblocks | 0.91b | 4 | 0.91b3 | ||
gemma | 0.98.4 | 5 | 0.98.52 | 0.98.4 0.98.32 0.98.1 | |
genome-painter | 0.0.8 | 2 | 0.0.8 | ||
gepard | 1.40 | 1 | |||
gfakluge | 1.1.2 | 1 | |||
gfalint | 1.0.0 | 1 | |||
gfaview | 0.0.53 | 1 | |||
Project | Selected | Spr | Newest | Outdated | Ignored |
gffcompare∗ | 0.12.1 | 5 | 0.12.62 | 0.12.2 0.10.15-1.be56ef4 | |
ghostz | 1.0.2 | 3 | 1.0.22 | ||
gmap-gsnap∗ | 2019-09-12 | 3 | 2019.03.15 | 2023-07-20 | |
groot | 1.1.2 | 2 | 1.0.2 1.0.0.r57.g05fe640 | ||
gzstream | 1.5 | 5 | 1.54 | 1.5+git20171107.9a20658 | |
harvest-tools | 1.3 | 2 | 1.3 | ||
hh-suite∗ | 3.3.0 | 4 | 3.3.03 | ||
hisat2 | 2.2.1 | 9 | 2.2.18 | 2.1.0 | 2.2.1.r55.g5086938 2.2.1+git20220316.1.5086938 |
hmmer | 2.4i | 17 | 3.48 | 3.3.29 3.3 3.2.1 3.1b22 3.1beta2 3.1_beta2 3.1b1 3.02 3 2.4i 2.3.23 | |
hssp∗ | 3.1.5 | 3 | 3.1.52 | ||
humann2∗ | 0.11.1 | 1 | |||
idba | 1.1.3 | 5 | 1.1.34 | 1.1.2 | 9999 1.1.3+git20161230.1.a1bafe6 |
indel-seq-gen | 2.1.03 | 2 | 2.1.03 | ||
indelible | 1.03 | 3 | 1.032 | ||
infernal | 1.1.3 | 8 | 1.1.52 | 1.1.46 1.1.3 1.1.2 1.1.1 1.1~rc4 1.0.22 | |
iqtree∗ | 1.6.12 | 7 | 2.2.2.74 | 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 | 3 | 2.2.2 | 2.1.3 | |
ispcr | 33 | 1 | |||
iva | 1.0.9 | 2 | 1.0.11 | 1.0.9 | |
ivar | 1.3 | 3 | 1.4.22 | 1.3.1 1.3 | |
jellyfish-k-mer∗ | 2.3.0 | 8 | 2.3.07 | 2.2.10 2.2.8 2.2.4 1.1.122 1.1.11 1.1.10 | |
jmol | 14.31.34 | 14 | 16.1.412 | 16.1.392 16.1.25 16.1.13 16.1.11 16.1.92 14.32.832 14.32.76 14.32.74 14.32.73 14.32.45 14.32.22 14.32.3 14.31.54 14.31.49 14.31.44 14.31.35 14.31.34 14.31.20 14.31.18 14.31.8 14.31.0 14.29.54 14.29.52 14.27.2 14.6.4+2016.11.05 14.6.0 14.2.9_2014.11.23 12.2.32 | |
jspecies | 1.2.1 | 1 | |||
k8 | 0.2.5 | 2 | 0.2.4 | ||
kaiju | 1.7.4 | 3 | 1.9.0 | 1.6.2 | |
kalign | 3.3 | 7 | 3.3.54 | 3.3.12 3.3 2.03+20110620 2.03 2.0.4 | 3.3.5+git20230204.1.90747e3 |
kat | 2.4.2 | 1 | |||
kent-tools∗ | 401 | 1 | |||
kma | 1.3.6 | 4 | 1.4.142 | 1.4.13 1.4.12 1.4.11 1.3.28 1.3.23 1.3.10 1.2.21 | |
kmc | 3.1.1 | 3 | 3.2.2 | 3.2.1+git20220114.1.a68b0c9 3.2.1 3.1.1 2.3 2.0 | |
kmergenie | 1.7048 | 2 | 1.7051 | ||
kounta | 0.2.3 | 1 | |||
kr-mutation-distances | 2.0.2 | 1 | |||
kraken∗ | 1.1.1 | 6 | 1.1.13 | 1.12 0.10.5~beta 0.1 | r70.2c5f7ce 32.368a837 1.1.1+git20210927.1.e75654f |
kraken2 | 2.1.1 | 6 | 2.1.32 | 2.1.2+git20211210.1.4f648f5 2.1.23 2.1.1 2.0.8~beta | |
kssd | 1.1 | 2 | 1.1 | ||
last | 1133 | 6 | 1499 | 1491 14713 1460 1453 1447 1411 1268 1260 1256 1179 1060 963 921 712 393 | |
lastz∗ | 1.04.03 | 6 | 1.04.225 | 1.04.15 1.04.032 | HEAD 1.04.22+git20221105.1.e66c1da |
legsta | 0.5.1 | 1 | |||
libbigwig | 0.4.4 | 8 | 0.4.75 | 0.4.6 0.4.43 | 9999 |
libccp4∗ | 6.5.1 | 7 | 8.0.02 | 6.5.15 6.4.6 6.4.5 | r1861 |
libdivsufsort | 2.0.1 | 13 | 2.0.112 | HEAD 2.0.1.14 | |
libgff | 2.0.0 | 6 | 2.0.05 | 1.0 | |
libpll | 0.3.2 | 3 | 1.0.11 | 0.3.2 0.3.1 | |
libsequence | 1.9.8 | 2 | 1.9.8 | ||
light-assembler | 1.0.0 | 1 | |||
lighter | 1.1.2 | 5 | 1.1.24 | 9999 | |
links-scaffolder | 1.8.7 | 1 | |||
lofreq | 2.1.3.1 | 2 | 2.1.5 | ||
lrsim | 1.0 | 1 | |||
Project | Selected | Spr | Newest | Outdated | Ignored |
lsd2 | 1.7.1 | 1 | |||
magic-blast∗ | 1.3.0 | 1 | |||
maker | 2.31.11 | 2 | 3.01.04 | ||
mapcaller | 0.9.9.39 | 2 | 0.9.9.39 | ||
mash-genome-distance | 2.2.2 | 5 | 2.33 | 2.2.2 2.12 2.0 | |
masurca | 3.4.1 | 3 | 4.1.02 | 4.0.1 | |
maxbin2 | 2.2.7 | 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 | 1.2.97 | 1.1.4 | 1.2.9+git20221006.1.769cfa2 |
meme-motif-discovery∗ | 5.1.0 | 4 | 5.5.42 | 5.5.1 | |
metabat | 2.15 | 5 | 2.153 | 0.32.4 | |
metaphlan∗ | 1.7.8 | 2 | 4.0.6 | 4.0.4 | |
mhap | 2.1.3 | 3 | 2.1.32 | 2.1.1 1.6 | |
mican | 2019.11.27 | 2 | 2019.11.27 | ||
minced | 0.4.2 | 4 | 0.4.22 | 0.3.2 | |
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 |
miniasm | 0.3 | 7 | 0.35 | 0.2 | 2018-3-30 0.3+git20191007.1.ce615d1 |
minigraph | 0.10 | 2 | 0.202 | ||
minimap | 0.2 | 2 | 0.2 | ||
minimap2∗ | 2.17 | 9 | 2.265 | 2.25 2.245 2.22 2.17 2.15 | 2.24.r39.g5e72423 |
mir-prefer | 0.24 | 1 | |||
mlst | 2.19.0 | 2 | 2.23.0 | ||
mmdb2∗ | 2.0.20 | 6 | 2.0.224 | 2.0.1 | |
mmtf-cpp∗ | 1.0.0 | 14 | 1.1.08 | 1.0.09 | |
mosdepth | 0.3.1 | 4 | 0.3.5 | 0.3.4 0.3.3+git20220502.1.556a460 0.3.32 0.3.2 0.3.1 0.2.3 | |
mothur | 1.44.3 | 6 | 1.48.04 | 1.47.0 1.44.3 1.42.1 1.39.5 1.36.1 1.31.2 1.27.0 1.41.21 | |
mp-est∗ | 2.0 | 1 | |||
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 |
mreps | 2.6.01 | 3 | 2.6.012 | ||
mummer | 3.23 | 7 | 4.0.0rc1 3.233 | 3.20 | 4.0.0.b2.2 |
muscle-sequence-alignment∗ | 3.8.1551 | 12 | 5.1.03 5.12 | 3.8.15515 3.8.315 | |
nanofilt∗ | 2.7.1 | 2 | 2.8.0 | 2.6.0+git20210224.1.76147c1 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 | 13 | 2.14.16 | 2.14.0 2.13.02 2.12.02 2.11.0 2.9.0 2.8.1 2.6.0 2.2.312 2.2.29 2.2.28 2.2.27 2.2.262 | |
newick-utils | 1.6 | 4 | 1.6 | 1.5.0 | 1.6-1.da121155 |
nextflow | 20.07.1 | 5 | 23.04.32 | 23.04.1 22.04.5 21.10.6 | |
nextgenmap | 0.5.5 | 1 | |||
ngmaster∗ | 0.5.6 | 1 | |||
ngmerge | 0.3 | 2 | 0.3 | ||
nonpareil-metagenomic-coverage | 3.3.4 | 1 | |||
ntcard | 1.2.2 | 3 | 1.2.22 | 9999 1.2.2+git20220105.1.9433d03 | |
ntedit | 1.3.4 | 1 | |||
nthits | 0.0.1 | 1 | |||
ntjoin | 1.0.6 | 1 | |||
nullarbor | 2.0.20191013 | 1 | |||
nxtrim | 0.4.3 | 3 | 0.4.32 | ||
oases | 0.2.08 | 1 | |||
oma | 2.4.2 | 1 | |||
orfm | 0.7.1 | 3 | 0.7.12 |
Legend: