Bioinformatics. Volume I. Data, sequence analysis, and evolution
DOI10.1007/978-1-4939-6622-6zbMath1378.92002OpenAlexW2885988310MaRDI QIDQ505398
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Publication date: 20 January 2017
Published in: Methods in Molecular Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1007/978-1-4939-6622-6
multiple sequence alignmentnatural selectiondatabase searchingontologiesassemblygenome sequencinggenetic recombinationgenome annotationgenomic databaseslarge-scale sequence comparisonlateral gene transferoptimal models of evolutionphylogenetic tree inferenceprotein crystallographyprotein domainssequence segmentationspecies tree estimation
Problems related to evolution (92D15) Collections of articles of miscellaneous specific interest (00B15) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10) Computational methods for problems pertaining to biology (92-08) Research exposition (monographs, survey articles) pertaining to biology (92-02)
Uses Software
- M-GCAT
- modENCODE
- GENCODE
- AceView
- GtRNAdb
- FlyBase
- Savant Genome Browser
- MEME-LaB
- piRNABank
- piRBase
- piRNAQuest
- lncRNAdb
- ModuleMaster
- MATCH
- Stampy
- NextGenMap
- HIVE-hexagon
- UCSC genome browser
- Ensembl REST
- BioStar
- TICO
- CRITICA
- GeneMarkS
- ZCURVE
- MOCAT
- GOLD
- Conrad
- CONTRAST
- mGene
- REGANOR
- ProtTest 3
- Partitionfinder
- DensiTree
- jModelTest
- CodonPhyML
- PhyloBayes 3
- SeqVis
- Bio++
- LDDist
- RDP2
- PhyloBayes MPI
- INDELible
- Hetero
- RAPSearch2
- BMGE
- CLANN
- ExaBayes
- TOPAL
- iGTP
- MulRF
- Tracer
- R
- ape
- Rfam
- BioJava
- ALLPATHS
- Biopython
- PHENIX
- PHYLIP
- MrBayes
- RAxML
- GOSim
- BIONJ
- MAFFT
- MODELTEST
- Spectronet
- Balibase
- Soap
- Cytoscape
- phytools
- HMMER
- bioperl
- PAML
- GOstat
- DIALIGN
- ClustalW
- SplitsTree
- BEAUti
- pIQPNNI
- LAGAN
- MUSCLE
- Kalign
- T-coffee
- VCFtools
- Samtools
- FASTA3
- PRALINE
- Cd-hit
- HHblits
- BLAT
- Mugsy
- Prodigal
- SPAdes
- Velvet
- IQ-TREE
- AVID
- SABmark
- FragGeneScan
- BioMart
- PCAP
- YACOP
- TRANSFAC
- MUMMER
- IGV
- FIMO
- BEDTools
- EasyGene
- MAKER
- InterProScan
- JBROWSE
- rBiopaxParser
- DendroPy
- AWTY
- Consed
- STRAP
- PatternHunter
- UniProt
- STRait Razor
- CCP4
- AMoRe
- MOLREP
- Coot
- GFF-Ex
- RamiGO
- ClueGO
- BioPortal
- kClust
- CLUSS
- CLAP
- PANTHER
- EVEREST
- CATH
- HAMAP
- PIRSF
- OrthoDB
- FunTree
- Gene3D
- M-Coffee
- Jalview
- SEAVIEW
- PHYLO_WIN
- CINEMA
- OXBench
- Cgaln
- FRESCO
- BRIG
- YASS
- CGView
- Dotlet
- JDotter
- BLASTZ
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