03-713 Bioinformatics Data Integration Practicum

Programming Resources

  1. Python documentation
  2. C++ STL
  3. Another C++ STL resource
  4. C++ BOOST libraries
  5. GitHub for source code version control
  6. SourceForge for source code version control
  7. Google Coding Style Guides
  8. Enthought Python distribution

Useful Software Libraries

  1. NetworkX - a Python graph library
  2. MatPlotLib - a Python matlab-like and plotting library
  3. iGraph - graph algorithms library
  4. NCBI C++ Toolkit
  5. Python Package Library
  6. SciPy - optimization and scientific computing library

Computing Resources

  1. Andrew/UNIX servers (do not run any large jobs on these machines)
  2. Virtual Andrew
  3. CMU Box Cloud Storage
  4. MacPorts - Ports of UNIX programs to the mac
  5. Cygwin - UNIX environment on Windows

Bioinformatics Software

  1. MAUVE - whole genome alignment with browser
  2. BLAST - sequence alignment and database search
  3. SplitsTree - phylogenetic network construction ***
  4. MrBayes - phylogenetic tree construction ***
  5. RAxML - phylogenetic tree construction
  6. Phylip - phylogenetic tree construction
  7. LAMARC
  8. CD-HIT - clustering DNA sequences
  9. DNACLUST - clustering DNA sequences
  10. MUSCLE - multiple sequence alignment
  11. GIRAF - Computational Identification of Influenza Reassortments ***
  12. JELLYFISH - fast k-mer counting
  13. BEAST - tree building
  14. SlidingBayes - recombination detection ***
  15. USEARCH - sequence-based search
  16. UCHIME - detection of chimeric sequences ***
  17. PILER - Genomic repeat analysis
  18. PALS - whole genome alignment
  19. MUMmer - whole gnome alignment
  20. Glimmer - bacterial gene finder
  21. HMMER - HMM-based alignment and search
  22. ERATE - Phylogenetic tree construction (handles indels)
  23. Archaeopteryx - tree viewing software
  24. AMOScmp - comparative genome assembly
  25. Bowtie - short read alignment
  26. A compressive list of recombination-detection software
  27. RDP - recombination detection program

Data Repositories

  1. NCBI Whole Genomes
  2. Antibiotic Resistance Genes Database ***

Tutorials and Courses

  1. Lawrence Hunter's article "Molecular Biology for Computer Scientists" (PDF)a
  2. NCBI Bookshelf (free biology textbooks)
  3. Bioinformatics course at UMD
  4. 02-710 Computational Genomics
  5. 02-223 How to analyze your own genome
  6. Theoretical Evolutionary Genetics by Joseph Felsenstein

Papers

  1. Huson et al. Reconstruction of Reticulate Networks from Gene Trees RECOMB 2005
  2. Posada D, Crandall KA. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl Acad. Sci. USA 2001;98:13757-13762.
  3. Martin DP, Williamson C, Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2005;21:260-262.
  4. Planet PJ. Tree disagreement: measuring and testing incongruence in phylogenies. J. Biomed. Inform. 2006;39:86-102.
  5. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006;22:1658-1659.
  6. Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001;17:754-755.
  7. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007;7:214.
  8. Paraskevis D, Deforche K, Lemey P, Magiorkinis G, Hatzakis A, Vandamme AM. SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. Bioinformatics 2005;21:1274-1275.