The elements of Bioinformatics The advantage is clear OPEN SOURCE TOOLS 90 Bn 08 So BLAST NCBi aligners (pairwise) SOAP 98 07 Hm Ma hMMER 81 KEY TO TOOL TYPE assemblers Genomic (Long Gene Prediction (mRNa) Workflows assemblers Genomic (Short Genome Browsers read) Py aligners (short read) read) Gene Prediction (ncRNa) Other aligners assemblers (mRNa) Sequence Tools ToolKit & aPis multiple Sequence aligners Structure modelling database / Warehouse Structure Visualisation Bs MAQ 99 Mu Bo MUMMER Ss 09 BWA 88 MAFFT 10 Sm FASTA SMALT 05 Ac ACT PRANK 02 04 12 RNA-STAR 10 Ja GMAP/GSNAP QUAKE 11 07 Al 07 Ve 12 Cn SPADES 96 09 CONTRAiL AUGUSTUS 12 MGENE 05 Ji PROT PAL METABiOME 08 Th 04 JiGSAW 12 Re TOPhAT 97 10 Ct 12 12 05 ENA 05 TOOLS fREE fOR aCadEmiCS ONLy 02 Bl 00 00 Vm Md BLAT VMATCh 92 01 Cm Sh CROSSMATCh MASKERAiD SSAhA2 11 Rt Av RNNOTATOR 09 Ab 11 Fg ANNOVAR 13 99 Gn FGENESh 03 97 GENSCAN 11 06 Bh GATK 89 Mt Mx Mk Mr Pro ABYSS MUTECT MEME MAKER MiRDEEP 09 GENBANK 97 Ga Pm BiOWAREhOUSE 08 NESTEDMiCA PROSiTE PAML 08 Pt Ip ChEMBAL 03 Cr Dl ChiMERA 09 UEA PYMOL Uc UCSC AA APSAMPLER GENABEL PhASTCONS 08 Ug UGENE XX Tp TRiPOD 09 00 Year of first release Xx Tool name TRANSMART 92 98 xx 07 Ts Tgp ThREADER 01 Ge Tm Td PCAP Sw Pm No PAThWAY TOOLS 01 12 04 10 10 ChEBiV Pc DALi 11 SRNA WORKBENCh 08 Vc 05 As MRBAYES SAVANT Cm Cb iNTERPRO 04 SEQMONK 02 Mb Pn Sv 09 VCFTOOLS 07 07 Qi 09 PiCARD ARTEMiS JBROWSE Sk PFAM 82 Dp Nm Gk DENDROPY Pf BiOPYThON 09 QiiME Pic At Jb DALLiANCE BROWSER 11 En FLExBAR Da 03 07 10 10 AMPLiCONNOiSE By ARGO 12 MiSO Nc Ag iGV Tg CATh Fb RSEM UNiPROT PSiPRED 07 04 99 Ps Ut Am NCBi-MAPViEWER Iv hhPRED SAMTOOLS UTGB 08 Up PDP JALViEW 03 05 09 Sa PLiNK iGB GBROWSE 10 MAUVE 04 02 SWiSS-MODEL 07 Pl Ig Gb KNiME Pd VARiANTTOOLS 08 71 Vt REPEATMASKER 08 11 02 APOLLO Kn ChADO Au Mg Mm Jv Po MUSCLE 09 10 LAGAN BiOPERL Ap GALAxY Ch STRELKA Rk SNAP 12 07 Ms BiSMARK 03 00 Bp ENSEMBL BROWSER 03 La Mve Hh BiORUBY Eb Gx iNTERMiNE St FASTxQC 11 Sn TRiNiTY 10 Ta 07 00 00 10 Bi BiOCONDUCTOR Br ENSEMBL APi 01 Bc BiOJAVA 00 03 TAVERNA In RNAFOLD Fq ENSEMBL PiPELiNE 10 Bj En EhiVE BiOMART Rn FASTx-TOOLKiT 00 10 09 Sp VELVET OASES Ty BAMBUS 2 09 09 00 03 Bm TRNASCAN Fx Ep 97 Tr CD-hiT EUGENE Oa Ba Cd 99 10 09 06 Eu CUFFLiNKS PE-ASSEMBLER Gl GLiMMER 3 Cu Pa 98 09 10 Co ALLPAThS-LG UNiGENE 09 08 10 03 Un SGA CORTEx_CON_RP Qu PRiCE 04 Ml MERACULOUS Pi FSA 95 RASMOL Me PhUSiON(2) Fs Sd SOAP: DE NOVO 10 03 08 Gm JALiGNER Ar Ph PROBCONS 11 FORGE ARAChNE Pb JMOL 09 02 05 09 Fo Rm Sg CELERA MAViD Rs 97 01 Jm SEQCLEAN Ce Ma Mv BFAST Fa Pr 04 Se MiRA 97 10 Cf 09 Bf ExONERATE 00 97 Mi PECAN T-COFFEE 05 Ex Pe CLUSTALW Bw SSAhA 06 Cl BOWTiE 03 94 EMBOSS Eh BiOSQL 08 00 Em PhYLiP 01 00 tm TMhMM 03 TARGETP 96 97 Mo Ro Sgp MODELLER ROSETTA SiGNALP #egelements COmmERCiaL TOOLS 08 Zm ZOOM 07 Ca CASAVA Oz OLiGOZiP 05 Ne NEWBLER 08 Gd GENEDATA 03 97 It iNTEGROMiCS Sr SRS 10 03 99 Gp Mh Mc GENEPOOL MATCh MASCOT 99 Pp PiPELiNE PiLOT 10 Gp GENExPLAiN 05 Gs GENESPRiNG Gu GENEiOUS PRO 05 Cb CLC BiO 10 An AViDASNGS 09 Pk PARTEK Dx PARTEK elements.eaglegenomics.com This table is distributed under the Creative Common License. It can be downloaded from our website. © Eagle Genomics Ltd 2012. All rights reserved. Eagle Genomics is a company registered in England and Wales. Company no. 6587071.
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