Projects

200 project(s) on this page

Project	Selected	Spr	Newest	Outdated	Ignored
abacas	1.3.1	4	1.3.13
adam∗	0.34.0	2			1.1.1
andi	0.13	7	0.145	0.13 0.12 0.9.6.1	0.14.3
any2fasta	0.4.2	4	0.4.23
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
astral-species-tree	5.7.1	4	5.7.13
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
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
bbtools∗	38.87	2	39.27	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
bioperl∗	1.007002	6	1.7.84	1.7.72 1.7.2 1.6.924 1.6.923 1.6.9	HEAD
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	13	1010	9 8
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
cd-hit∗	4.8.1	11	4.8.19	4.6.8 4.6.6 4.6.4 4.6.1-2012-08-27
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
circos∗	0.69-9	7	0.69.92 0.69-92 0.69_9	0.69.6 0.69 0.64 0.49
clonalframeml	1.12	3	1.132	1.12 1.11
clustal-omega∗	1.2.4	12	1.2.410	1.2.2 1.2.1
clustalw∗	2.1	15	2.112	1.832	2.1+lgpl 2.1+lgpl
consel	0.20	3		0.1	2011.05.12
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 6.3.1.2 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
discovardenovo∗	52488	2	52488
disty	0.1.0	2	0.1.0
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
edirect∗	13.8	3		13.3.20200128	24.2.20250612
elph	1.0.1	5	1.0.14
emboss∗	6.6.0	15	6.6.012	6.5.7 6.4.0 6.0.1
exabayes	1.5	3	1.5.12
exonerate	2.4.0	11	2.4.09	2.2.02
Project	Selected	Spr	Newest	Outdated	Ignored
express-rna-seq	1.5.3	3	1.5.32
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	0.26.03	0.24.2 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
fastq-pair	1.0	3	1.02
fasttree	2.1.11	9	2.1.117	2.1.102 2.1.9 2.1.8 2.1.7
fastuniq	1.1	2	1.1
fermi-lite	0.1	4	0.1	0.1.r13.g85f159e	0.1.13 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
finch-rs∗	0.3.0	2	0.6.0
flash-seq∗	1.2.11	6	1.2.115
flye∗	2.8.3	3	2.9.62	2.9.52 2.9.42 2.9.3 2.9.1	HEAD
fraggenescan	1.31	2	1.31
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
gblocks	0.91b	4	0.91b3
gemma	0.98.4	5	0.98.53	0.98.4 0.98.3 0.98.1
genome-painter	0.0.8	2	0.0.8
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.r85.gca6c8f2
gzstream	1.5	5	1.54		1.5+git20171107.9a20658 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
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
hssp∗	3.1.5	3	3.1.52
idba	1.1.3	5	1.1.34	1.1.2	9999
indel-seq-gen	2.1.03	2	2.1.03
indelible	1.03	3	1.032
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	16.3.27	16.3.25 16.3.232 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
k8	0.2.5	2		0.2.4
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
kraken	1.1.1	6	1.1.13	1.1 0.10.5~beta 0.1	r70.2c5f7ce 32.368a837
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
Project	Selected	Spr	Newest	Outdated	Ignored
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
libgff	2.0.0	7	2.0.06	1.0
libpll	0.3.2	4	1.0.11	0.3.22 0.3.1
libsequence	1.9.8	2	1.9.8
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	5.5.8	5.5.72 5.5.42
metabat	2.15	4	2.153
metaphlan∗	1.7.8	2	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	3	0.4.2	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
minigraph	0.10	2	0.212
minimap∗	0.2	3	0.2	0-unstable-2024-11-23
minimap2∗	2.17	9	2.294	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
mreps	2.6.01	3	2.6.012
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
newick-utils	1.6	3	1.6		1.6-1.da121155
nextflow	20.07.1	5	25.04.3	25.04.2 24.08.0-edge 24.04.3 22.04.5
ngmerge	0.3	2	0.3
ntcard	1.2.2	3	1.2.22		9999
nthits	0.0.1	2	1.0.2
nxtrim	0.4.3	3	0.4.32
orfm	0.7.1	3	0.7.12
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
pandaseq	2.11	3	2.112
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
Project	Selected	Spr	Newest	Outdated	Ignored
pathvisio	3.3.0	2	3.3.0
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
phylobayes	4.1e	2	4.1e	4.1c
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
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
porechop	0.2.4	3	0.2.4	0.2.3-1.289d5dc
portcullis	1.1.0	2	1.2.3
pplacer	1.1.alpha17	3	1.1~alpha19 1.1.alpha19
prank∗	170427	7	1704274	140603 0.0.170427 0.0.150803 0.0.140110
prokka	1.14.6	3	1.14.62	1.14.5
psmc	0.6.5	3	0.6.5		2016-1-21
pullseq	1.0.2	2	1.0.2
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 20250603-7ef781c0 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	3.10.317	3.10.18 3.10.02 3.9.43 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
quicktree	2.5	3	2.52
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
raster3d	3.0-7	5	3.0.7 3.0-7	3.0.6 3.0-4 3.0-3 3.0-2 3.0
raxml∗	8.2.12	9	8.2.134	8.2.126 8.2.11 8.2.4 7.2.8
rcorrector	1.0.4	2	1.0.4
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
roary	3.13.0	4	3.13.02	3.12.02 3.6.0
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▲
salmid	0.1.23	2	0.1.23
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
samblaster	0.1.26	6	0.1.265	0.1.24
samclip	0.4.0	3	0.4.02
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
seq-gen	1.3.4	4	1.3.42	1.3.32
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 2.5.02 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
sga	0.10.15	4	0.10.152		9999
shovill	1.1.0	2	1.1.0
sibelia	3.0.7	2	3.0.7
ska-split-kmer	1.0	3	1.02
skesa	2.4.0	3	2.4.02	2.3.0
slim-simulator∗	3.5	3	5.0	5.0.r0.gacf0f088
smalt	0.7.6	5	0.7.64
snap-gene-prediction∗	2013-11-29	2	20131129
snippy	4.6.0	3	4.6.02

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.