| 1. Genome assembly (de novo) |
ALLPATHS_LG |
http://www.broadinstitute.org/software/allpaths-lg/blog/ |
211 |
| SOAPdenovo2 |
http://soap.genomics.org.cn/soapdenovo.html |
212 |
| 2. Assembly statistics |
FASTQC |
www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
|
|
3. Gene annotationa
|
GENSCAN |
http://genes.mit.edu/GENSCAN.html |
213 |
| AUGUSTUS |
http://bioinf.uni-greifswald.de/augustus/ |
214 |
| Gnomon |
http://www.ncbi.nlm.nih.gov/genome/guide/gnomon.shtml |
|
| Genewise |
http://www.ebi.ac.uk/~birney/wise2/ |
216 |
| Exonerate |
http://www.ebi.ac.uk/~guy/exonerate/ |
217 |
| Splign |
http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi |
218 |
| 4. DNA variants |
|
|
|
| a. SNPs |
SAMtools |
http://samtools.github.io/ |
219 |
| VCFtools |
http://vcftools.sourceforge.net/ |
220 |
| GATK |
https://www.broadinstitute.org/gatk/ |
221 |
| b. Indels |
BreakDancer |
http://breakdancer.sourceforge.net/ |
222 |
| VariationHunter |
http://compbio.cs.sfu.ca/software-variation-hunter |
223 |
| Picard |
http://sourceforge.net/projects/picard/ |
|
| c. Copy number variationb
|
Cortex assembler |
http://cortexassembler.sourceforge.net/index_cortex_var.html |
224 |
| Magnolya |
http://sourceforge.net/projects/magnolya/ |
225 |
| mrCaNaVaR |
http://mrcanavar.sourceforge.net |
226 |
| cn.MOPS |
http://www.bioinf.jku.at/software/cnmops/ |
227 |
| 5. Repetitive element content |
|
|
|
| a. Interspersed repeats |
RepeatMasker |
http://www.repeatmasker.org |
|
| WindowMasker |
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ |
228 |
| b. Tandem repeatsc
|
Tandem Repeats Finder |
http://tandem.bu.edu/trf/trf.html |
229 |
| c. Microsatellites |
Misa |
http://pgrc.ipk-gatersleben.de/misa/ |
232 |
| GMATo |
http://sourceforge.net/projects/gmato/files/ |
233 |
| d. Low-complexity regions |
DustMasker |
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/dustmasker/ |
230 |
| 6. Endogenous retrovirus-like elements |
RetroTector |
http://retrotector.neuro.uu.se/ |
234 |
| LTR_STRUC |
http://www.mcdonaldlab.biology.gatech.edu/ltr_struc.htm |
235 |
| LTR-FINDER |
http://tlife.fudan.edu.cn/ltr_finder/ |
236 |
| LTRharvest |
http://www.zbh.uni-hamburg.de/?id5206 |
237 |
| 7. Segmental duplications |
Dupmasker |
http://www.repeatmasker.org/DupMaskerDownload.html |
238 |
| 8. MicroRNAs |
MiRFinder |
http://www.bioinformatics.org/mirfinder/ |
240 |
| miRBase |
http://www.mirbase.org/ |
241 |
| ViennaRNA |
http://www.tbi.univie.ac.at/RNA/index.html |
242 |
| 9. Methylation sites |
Bismark |
http://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
244 |
| BS Seeker |
http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html |
245, 246
|
| FadE |
https://code.google.com/p/fade/ |
247 |
| 10. Gene family expansion and contraction |
CAFÉ |
http://sites.bio.indiana.edu/~hahnlab/Software.html |
250, 251
|
| 11. Evolutionary constrained elements |
phastCons |
http://compgen.bscb.cornell.edu/phast/phastCons-HOWTO.html |
252 |
| SiPhy |
http://www.broadinstitute.org/genome_bio/siphy/index.html |
254 |
|
12. Signature of Selectiond
|
|
|
|
| a. Ds/Dn ratios |
PAML 4 |
http://abacus.gene.ucl.ac.uk/software/paml.html |
255 |
| b. Fst outliers |
LOSITAN |
http://popgen.net/soft/lositan/ |
256 |
| c. Homozygous tracks |
PLINK |
http://pngu.mgh.harvard.edu/~purcell/plink/ |
257 |
| d. Extended haplotypes |
rehh |
http://cran.r-project.org/web/packages/rehh/index.html |
258 |
| 13. Transcriptome mapping |
|
|
|
| a. Assembler |
Trinity |
http://trinityrnaseq.sourceforge.net/ |
259 |
| b. Aligner |
TopHat |
http://ccb.jhu.edu/software/tophat/index.shtml |
260 |
| STAR |
https://code.google.com/p/rna-star/ |
261 |
| 14. Comparative assessment; HSBs, EBRs |
Evolution Highway |
http://eh-demo.ncsa.uiuc.edu/ |
262, 263
|
| Satsuma |
http://sourceforge.net/projects/satsuma/ |
264 |
| SyMAP |
http://www.agcol.arizona.edu/software/symap/ |
265 |
| RACA |
http://bioen-compbio.bioen.illinois.edu/RACA/ |
270 |
| 15. Genome alignment |
MultiZ |
http://www.bx.psu.edu/miller_lab/dis....012109.tar.gz |
52 |
| LASTZ |
http://www.bx.psu.edu/~rsharris/lastz/ |
266 |
| 16. Genome browsers |
GBrowse |
http://gmod.org/wiki/GBrowse |
132 |
| JBrowse |
http://jbrowse.org/ |
133 |
| UCSC Genome Browser |
http://genome.ucsc.edu |
134, 267
|
| Integrative Genomics Viewer (IGV) |
https://www.broadinstitute.org/igv/home |
268, 269
|
