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Tools For Phylogenic Analysis

#RAxML - Randomized Axelerated Maximum Likelihood
  http://sco.h-its.org/exelixis/web/software/raxml/
  https://github.com/stamatak/standard-RAxML
  Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9), 1312-1313.

#PAML - Phylogenetic Analysis by Maximum Likelihood
  http://abacus.gene.ucl.ac.uk/software/paml.html
  Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Molecular biology and evolution, 24(8), 1586-1591.
  
#ETE Toolkit - Analysis and Visualization of (phylogenetic) trees
  http://etetoolkit.org/
  Huerta-Cepas, J., Dopazo, J., & Gabaldón, T. (2010). ETE: a python Environment for Tree Exploration. BMC bioinformatics, 11(1), 24.

Tools For Gene Ontology Analysis

#topGo - R Bioconductor Package for testing GO terms 
  https://bioconductor.org/packages/release/bioc/html/topGO.html
  Alexa A and Rahnenfuhrer J (2016). topGO: Enrichment Analysis for Gene Ontology. R package.

Sequence Alignment Tools

#Comparision

  • Accuracy: BLAST > BLAT > Bwa > Bowtie

  • Speed: Bowtie > Bwa > BLAT > BLAST