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Project	Selected	Spr	Newest	Outdated	Ignored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	4	0.143	0.13 0.12 0.9.6.1
any2fasta	0.4.2	4	0.4.23
aragorn	1.2.38	5	1.2.414	1.2.382 1.2.36
arcs	1.2.1	2	1.2.2
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	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
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
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
bfc	r181	5	1.12.0	1.0.1 0.2 g20150417
bifrost	1.0.5	3	1.2.1	1.0.5
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
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
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
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
consel	0.20	3		0.1	2011.05.12
cutadapt∗	3.3	4	4.4	4.0 1.14
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
dssp∗	3.1.4	10	4.4.23	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
edirect∗	13.8	2		13.3.20200128
elph	1.0.1	5	1.0.14
emboss∗	6.6.0	15	6.6.011	6.5.7 6.4.0 6.0.1
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
Project	Selected	Spr	Newest	Outdated	Ignored
falco-fastqc	0.2.4	2	1.2.1
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
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
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
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
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
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
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
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
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
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
libbigwig	0.4.4	8	0.4.75	0.4.6 0.4.43	9999
Project	Selected	Spr	Newest	Outdated	Ignored
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
lighter	1.1.2	5	1.1.24		9999
lofreq	2.1.3.1	2	2.1.5
maker	2.31.11	2	3.01.04
mapcaller	0.9.9.39	2	0.9.9.39
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
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
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
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
ngmerge	0.3	2	0.3
ntcard	1.2.2	3	1.2.22		9999 1.2.2+git20220105.1.9433d03
nxtrim	0.4.3	3	0.4.32
orfm	0.7.1	3	0.7.12
paml∗	4.9j	10	4.10.73	4.10.6 4.10.3 4.9j4 4.9h 4.9g 4.9e 4.8 4.7 4.4e
pandaseq	2.11	3	2.112
parasail	2.4.2	2	2.6.2	2.6 2.5 2.4.3
parsnp	1.5.2	2	1.7.4	1.6.2 1.5.4 1.2.1 1.2
pathvisio	3.3.0	2	3.3.0
peat	1.2.5	2		1.0.2
percolator	3.05	4	3.06.012	3.05 3.04 3.3 3.03 3.02.01 3.02.00 3.01	3.06.01
Project	Selected	Spr	Newest	Outdated	Ignored
phylip	3.697	9	3.6982	3.6975 3.696 3.695 3.692
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	r121.ab59039 201204122
phyx	1.01	3	1.3.12	1.3 1.01 0.999
pilon	1.23	4	1.242	1.23 1.22
pirate	1.0.4	2	5.6.0
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 v1.90b6.26	1.9.r40.gdcc7785a 1.90_pre140514 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	6	1704273	140603 0.0.170427 0.0.150803 0.0.140110
prokka	1.14.6	3	1.14.62	1.14.5	1.14.6+git20200804.1.c335b7a
psmc	0.6.5	3	0.6.5		2016-1-21
pullseq	1.0.2	2	1.0.2
pymol	2.4.0	19	2.5.013	2.4.1 2.4.04 2.3.3 2.3.05 2.2.02 2.1.0 1.9.0.0.svn4184 1.8.6.0 1.8.6 1.8.4.0 1.7.7.1.svn4131 1.7.4.0 1.7.2.1 1.7.0.0 1.4.1	r4806.c7095ec2 HEAD 20230728-5622d761 2.5.5 2.5.2 2.5.1 2.5.0.97
python:matplotlib∗	3.3.4	40	3.8.012	3.7.36 3.7.29 3.7.15 3.7.0 3.6.34 3.6.24 3.6.0 3.5.34 3.5.24 3.5.15 3.5.0 3.4.35 3.4.22 3.4.1 3.3.42 3.3.34 3.3.2 3.2.2 3.2.14 3.1.3 3.1.22 3.1.1 3.0.32 3.0.2 2.2.56 2.2.43 2.2.33 2.1.2 2.1.1 2.0.2 2.0.0 1.5.13 1.4.3 1.3.12 1.2.1 1.2.02 0.99.1.22	r26679.b9b02f189
quast	5.0.2	2	5.0.2
quicktree	2.5	3	2.52
quip	1.1.8	2	8.4.4
racon	1.4.13	5	1.5.02	1.4.20 1.4.10 1.4.32 1.3.2	1.5.0.r0.ga2cfcac
raptor∗	1.1.0	39	2.0.1616	2.0.1529 2.0.14.1 2.0.14 2.0.13 2.0.92 2.0.8 2.0.3 2.0.2 2.0.0 1.4.2111 1.4.20 1.4.19 1.4.18 0~git20221211	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	8.2.127	8.2.11 8.2.4 7.2.8 7.2.6
rcorrector	1.0.4	2	1.0.4
repeatmasker∗	4.0.7	3	4.1.52
rmblast	2.2.28	2	2.2.28
rna-star	2.7.5c	11	2.7.11a3	2.7.11.a 2.7.10b5 2.7.10a3 2.7.9a 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	2	3.12.1
ruby:rails∗	1.5.1▲	23	7.0.87	7.0.7.23 7.0.7 7.0.5.12 7.0.4.33 7.0.2.3▲2 7.0.1▲ 6.1.7.63 6.1.7.4 6.1.7.3 6.1.7.2 6.1.7.1 6.1.4.7▲ 6.1.4.4▲ 6.1.4.1▲3 6.1.4▲ 6.1.3.2▲ 6.1.2.1▲ 6.0.6.1 6.0.3.7▲ 6.0.3.4▲ 6.0.3.3▲ 6.0.2.2▲ 5.2.8.1▲ 5.2.4.3▲ 5.2.4.1▲ 5.2.3▲3 5.2.2.1▲ 5.2.2▲ 5.2.1▲2 5.1.7▲ 5.1.6▲ 5.1.5▲ 5.1.4▲2 5.0.7.2▲ 5.0.2▲ 4.2.11.3▲ 4.2.10▲ 4.2.6▲2 4.2.5.1▲ 4.2.4▲ 4.1.1▲ 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	7	1.10.24	1.10.12 1.9.0 1.4.0 1.2.2 0.12.0 0.7.2
sambamba	0.7.1	6	1.0.13	1.0.0 1.0 0.8.24 0.8.1 0.8.0 0.6.7 0.6.6
samblaster	0.1.26	6	0.1.264	0.1.242
samclip	0.4.0	3	0.4.02
sdsl-lite∗	2.1.1	8	3.0.2	3.0.1 3.0.0 2.3.1 2.1.1.137 2.1.14 2.0.3 v2.1.1.r132.gddb0fbbc
sepp	4.3.10	3	4.5.1	4.3.10	4.5.1+really4.5.1
seq-gen	1.3.4	4	1.3.42	1.3.32	1.3.4+git20190829.1.e8660d7
seqan	3.0.2 2.4.0	12	3.3.03	3.3.0~rc2 3.3.0-rc2 3.2.04 3.1.04 3.0.33 3.0.22 3.0.1 2.4.09 2.3.2 1.4.24 1.4.1 1.3.12	3.0.0.r465.g4cdd84b2
seqkit	0.15.0	7	2.5.15	2.4.0 2.3.12 2.3.0+git20220823.1.6a62d6c 2.1.0 0.15.0 0.10.1	HEAD
sga	0.10.15	5	0.10.153		9999
shovill	1.1.0	2	1.1.0		1.1.0+git20200803.1.f64d19e
sibelia	3.0.7	2	3.0.7
ska-split-kmer	1.0	3	1.02		1.0+git20190123.1.03eed54
skesa	2.4.0	3	2.4.02	2.3.0
slim-simulator∗	3.5	3	4.0		4.0.1.r0.g503b8b20
smalt	0.7.6	4	0.7.63		0.7.6+git20140509.1.40f599e
snap-gene-prediction∗	2013-11-29	2	20131129
snippy	4.6.0	3	4.6.02
snp-dists	0.7.0	2	0.7.0

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.