Projects

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Project	Selected	Spr	Newest	Outdated	Ignored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:

• Spread means how many repository families (e.g. all Debian versions as well as Ubuntu and other derivatives make a single family) contain this package.
• newest^#repos - newest known version. The number shows how many repository families have this version.
• devel - newest known devel (or unstable) version. There may be both devel and newest versions for a given package.
• unique - package is only present in a single repository family, there are no other sources to compare it against, so although it's the latest version known to repology, is not really reliable.
• outdated - outdated version which requires updating.
• legacy - outdated version when a newer version is present. This is assumed to be legacy version preserved for e.g. compatibility.
• rolling - package is fetched from always latest snapshot or VCS master/trunk, so it is always latest and is not a subject for comparison.
• noscheme - the project does not have official versioning scheme, so versions used in repositories which are basically random.
• incorrect - version is known to be incorrect (e.g. version not officially released yet, or lacking alpha/beta/rc qualifier).
• untrusted - this source is known to likely supply incorrect versions, so is ignored proactively.
• ignored - version is ignored and excluded from comparison for some other reason (e.g. snapshots).
• vulnerable▲ - version is potentially vulnerable as there are related CVEs.