Projects

132 project(s) on this page

Project	Selected	Spr	Newest	Outdated	Ignored
adam∗	0.34.0	2	1.1.1
andi	0.13	4	0.143	0.13 0.12 0.9.6.1
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
bali-phy	3.6.0	4	4.0~beta2 3.6.13	3.6.0 3.4.1 3.4	4.0-beta6
bandage	0.8.1	5	0.9.03	0.8.12
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
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	1.3.110	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
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
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
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
exabayes	1.5	3	1.5.12	1.4.1
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
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
flye∗	2.8.3	2	2.9.2	2.9.1
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
gemma	0.98.4	5	0.98.52	0.98.4 0.98.32 0.98.1
gffcompare∗	0.12.1	5	0.12.62	0.12.2 0.10.15-1.be56ef4
hmmer	2.4i	16	3.46	3.3.210 3.3 3.2.1 3.1b22 3.1_beta2 3.1b1 3.02 3 2.4i 2.3.23
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
jmol	14.31.34	14	16.1.41	16.1.39 16.1.353 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
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
Project	Selected	Spr	Newest	Outdated	Ignored
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
kraken2	2.1.1	6	2.1.32	2.1.2+git20211210.1.4f648f5 2.1.23 2.1.1 2.0.8~beta
last	1133	6	1491	14713 1460 1453 1447 1411 1282 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
libccp4∗	6.5.1	7	8.0.02	6.5.15 6.4.6 6.4.5	r1861
libpll	0.3.2	3	1.0.11	0.3.2 0.3.1
lofreq	2.1.3.1	2	2.1.5
maker	2.31.11	2	3.01.04
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	8	22.282 22-282	14-1373 14.1372 14_137 12-135 1.008.09.149
meme-motif-discovery∗	5.1.0	4	5.5.42	5.5.1
metaphlan∗	1.7.8	2	4.0.6	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	0.202
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
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
nextflow	20.07.1	5	23.04.32	23.04.1 22.04.5 21.10.6
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
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
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
phylip	3.697	9	3.6982	3.6975 3.696 3.695 3.692
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
portcullis	1.1.0	2	1.2.3
pplacer	1.1.alpha17	3	1.1~alpha19 1.1.alpha19
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	39	3.8.011	3.7.35 3.7.211 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
quip	1.1.8	2	7.75.3
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	38	2.0.1615	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
repeatmasker∗	4.0.7	3	4.1.52
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
Project	Selected	Spr	Newest	Outdated	Ignored
rtg-tools	3.11	2	3.12.1
ruby:rails∗	1.5.1▲	23	7.0.86	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▲
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
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
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
slim-simulator∗	3.5	3	4.0		4.0.1.r0.g503b8b20
snap-gene-prediction∗	2013-11-29	2	20131129
snpeff	4.3t	8	5.13	4.3t3	2017-11-24 5.1+d
sortmerna	2.1	5	4.3.6	4.3.4 4.2.0 2.1 2.0	2017-07-13 4.3.6+git20221026.1.2ac819a
stacks	2.41	9	2.65	2.622 2.604 2.59 2.55 2.53 2.41 2.4 2.2 2.1 2.0Beta8c 1.35 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	1.15.0	1.14.15 1.14.14 1.14.13 1.14.11 1.14.9 1.14.82 1.14.6 1.13.5 1.12.4
stringtie	2.1.4	10	2.2.14	2.2.0 2.1.5 2.1.4 2.1.13 1.3.6
subread	2.0.1	8	2.0.64	2.0.5 2.0.4 2.0.34 2.0.2 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		0.15.0
tigmint	1.2.2	2	1.2.4
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
trinityrnaseq	2.11.0	4	2.15.1	2.15.1.FULL 2.13.22 2.11.0 2.6.6 2.5.1
trnascan-se	2.0.4	6	2.0.122	2.0.112 2.0.10 2.0.9 2.0.7 2.0.5 2.0.0 1.31 1.3.1
unicycler∗	0.4.7	3	0.5.02	0.4.8 0.4.7
unikmer	0.11.0	3	0.19.12	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	1.0.92	1.0.7 1.0.3	1.0.3.r330.ga36dbe9
viennarna∗	2.4.17	7	2.6.33	2.5.1 2.5.0 2.4.18 2.4.17
vt	0.5772	6	0.577212	0.57722	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.