Year


Xx


NAME

KEY TO TOOL TYPE (stripes indicate new update)
Aligners (pairwise) Gene Prediction (mRNA)
Aligners (short read) Gene Prediction (ncRNA)
Other Aligners Sequence Tools
Multiple Sequence Aligners Database/Warehouse
Assemblers Genomic (long read) Workflows
Assemblers Genomic (short read) Genome Browsers
Assemblers (mRNA) ToolKits and APIs
Structure Modelling Structure Visualisation

Open Source Tools

90


Bn


BLAST NCBI

08


So


SOAP

81


Py


PHYLIP

00


Em


EMBOSS

00


Bj


BIOJAVA

01


Bc


BIOCONDUCTOR

10


Bi


Bismark

03


Ms


SWISS-MODEL

98


Hm


HMMER

07


Mq


MAQ

01


Bs


bioSQL

00


Eh


eHIVE

00


En


ENSEMBL API

00


Br


bioRUBY

03


La


LAGAN

10


Mve


Mauve

05


Hh


HHpred

99


Mu


MUMmer

08


Bo


Bowtie

94


Cl


CLUSTALW

06


Pe


PECAN

97


Mi


MIRA 97

04


Se


SEQCLEAN

01


Jm


Jmol

09


Sd


SOAP: DE NOVO 2

03


Un


UNIGENE

98


Gl


GLIMMER 3

06


Cd


CD-HIT

97


Tr


tRNAscan

03


Bm


bioMART

03


Ta


TAVERNA

00


Eb


ENSEMBL BROWSER

00


Bp


bioPERL

07


Pl


PLINK

09


Sa


SAMtools

99


Ps


PSIPRED

03


Ss


SSAHA

09


Bw


BWA

00


Cf


T-COFFEE

10


Pr


PRANK

97


Ce


CELERA

09


Fo


FORGE

95


Rm


RasMol

09


Sg


SGA

09


Cu


CUFFLINKS

99


Eu


EUGENE

09


Fx


FASTX-Toolkit

10


Rn


RNAfold

07


In


INTERMINE

07


Gx


GALAXY

02


Ap


APOLLO

04


Ig


IGB

07


Ut


UTGB

10


Am


AMPLICONNOISE

09


Qi


QIIME

05


Ex


EXONERATE

09


Bf


BFAST

02


Ma


MAFFT

04


Mv


MAVID

02


Ar


ARACHNE

10


Me


MERACULOUS

08


Co


CORTEX_CON_RP

10


Pa


PE-ASSEMBLER

10


Oa


OASES

00


Ep


ENSEMBL PIPELINE

10


Fq


FastQC

12


St


Strelka

10


Ch


CHADO

08


Kn


KNIME

02


Gb


GBROWSE

04


Nc


NCBI MapViewer

03


By


BioPython

09


Pic


Picard

09


Vc


VCFtools

88


Fa


FASTA

10


Sm


SMALT

12


Rs


rna-star

05


Pb


PROBCONS

03


Ph


PHUSION(2)

10


Qu


QUAKE

07


Al


ALLPATHS-LG

09


Ba


BAMBUS 2 09

11


Ty


Trinity

11


Sn


SNAP

96


Rk


RepeatMasker

11


Vt


VariantTools

71


Pd


PDB

03


Up


UniProt

08


Iv


IGV

07


Ag


ARGO

02


At


ARTEMIS

05


As


APSampler

12


Ge


GenABEL

05


Ac


ACT

10


Ja


JAligner

11


Gm


GMAP/GSNAP

08


Fs


FSA

11


Pi


PRICE

07


Ve


VELVET

12


Sp


SPAdes

09


Cn


Contrail

09


Au


AUGUSTUS

08


Mg


MGENE

09


Mm


MetaBioME

04


Jv


JalView

97


Ct


CATH

12


Tg


MISO

10


Da


DALLIANCE BROWSER

07


Jb


JBROWSE

XX


Mb


MrBayes

04


Pn


PhastCons

08


Ug


UGENE

04


Ml


MUSCLE

12


Po


PROT PAL

05


Ji


JIGSAW

08


Th


Tophat

12


Re


RSEM

12


Fb


Flexbar

12


Ea


ENA

11


Pf


Pfam

07


Sk


SeqMonk

10


Sv


Savant

XX


Tp


Tripod

10


Dp


DendroPy

05


Nm


NestedMICA

82


Gk


Genbank

05


Ip


Interpro

08


Cm


ChEMBL

10


Cb


ChEBI

09


Tm


tranSMART

Tools Free for Academics Only

02


Bl


BLAT

00


Vm


VMATCH

00


Md


MaskerAid

11


Rt


Rnnotator

11


Av


ANNOVAR

99


Fg


FGENESH

97


Gn


GENSCAN

06


Bh


BioWarehouse

09


Ga


GATK

97


Pm


PAML

04


Cr


Chimera

03


Dl


Dali

01


Pc


PCAP

92


Td


THREADER

98


Ts


TMHMM

07


Tgp


targetP

92


Cm


CROSSMATCH

01


Sh


SSAHA2

09


Ab


ABYSS

13


Mt


MuTect

03


Mx


MEME

11


Mk


MAKER

08


Mr


MiRDeep

89


Pro


PROSITE

08


Pt


Pathway Tools

11


Sw


sRNA workbench UEA

XX


Pm


PyMOL

09


No


NOVOALIGN

01


Uc


UCSC

03


Mo


Modeller

96


Ro


ROSETTA

97


Sgp


signalP

Commercial Tools

08


Zm


ZOOM

XX


Ca


Casava

08


Gd


Genedata

03


It


Integromics

97


Sr


SRS

10


Gp


geneXplain

10


An


Avadis NGS

XX


Pk


Partek

09


Dx


DNANexus

07


Oz


OLIGOZIP

05


Ne


NEWBLER

10


Gp


GenePool

03


Mh


Match

99


Mc


Mascot

99


Pp


PIPELINE PILOT

XX


Gs


GENESPRING

05


Gu


Geneious

05


Cb


CLC BIO

Tweets about "#egelements"