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Tools

Here's a place for me to remember tools that have come in handy or I have used and want to remember for future work. This list is a work in progress.

General Tools

*Victorian Bioinformatics Consortium *Explain SAM flags *Seqtk *bedtools *homebrew science (linux brew) *GSL *bioawk *bioawk-tools *khmer *screed *Pear *pandaseq

Genome Assembly

*mix (on github) *Pilon

Comparative Genomics

*lastz *Proteinortho *Fripan

Amplicon Analysis

*MED *Oligotyping *QIIME / MacQIIME *mothur *denoiser *amplicon noise *clovr-ITS *Topiary Explorer *phylosift *otupipe

Metagenomics

*Anvi'o *CONCOCT *FishTaco

Ortholog & Synteny analysis

*FriPan - ortholog visualization *InParanoid *OrthoMCL *ProteinOrtho *QuickParanoid *symap

Phylogenetics

Using R for phylogenetics: Tools, Tutorials, and recommendations

*Brian O'Meara Lab R for Phylogenetics Tutorial *CRAN Task View: Phylogenetics, Especially Comparative Methods *ggtree - package for plotting phylogenetics trees via ggplot2 *r-phylo.org wiki page *FigTree *Spread *PhyDE *SplitsTree *dendropy *beast *ETE2

Transcriptomics

organize and provide links for these:

*stacks *MYSQL *fastx-toolkit *d3-javascript *cytoscape *IGV *GATK toolkit *StrapAlign