Works Cited

[grabear]

Go through different code and preform work cited where necessary in a md or rst document.
Comment code with Work Cited Index numbers.
Do research to see if there is a standard way to do works cited for programming projects.

    Format:
{
file: 'file',
path: 'path',
line: 000,
citation: 'biopython',
etc: 'etc'
}

[sdhutchins]

I think this is just going to come down to adding in citations from the services/programs we used.

• Guidance2
• Pal2nal
• IQTree
• Clustal Omega
• Biopython
• ETE
• PhyML
• Treelib?
• BioSQl?

Feel free to add more or the rest.

[grabear]

I think this is just going to come down to adding in citations from the services/programs we used.

• Guidance2
  When citing the GUIDANCE2 server please refer to:
  Sela, I., Ashkenazy, H., Katoh, K. and Pupko, T. (2015)
  GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of
  multiple parameters.
  Nucleic Acids Research, 2015 Jul 1; 43 (Web Server issue): W7-W14.; doi: 10.1093/nar/gkq443

  Landan, G., and D. Graur. (2008).
  Local reliability measures from sets of co-optimal multiple sequence alignments.
  Pac Symp Biocomput 13:15-24 [ABS] [PDF]

  Penn, O., Privman, E., Ashkenazy, H., Landan, G., Graur, D. and Pupko, T. (2010).
  GUIDANCE: a web server for assessing alignment confidence scores.
  Nucleic Acids Research, 2010 Jul 1; 38 (Web Server issue):W23-W28; doi: 10.1093/nar/gkq443

  When using the GUIDANCE2 algorithm please cite:
  Sela, I., Ashkenazy, H., Katoh, K. and Pupko, T. (2015)
  GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of
  multiple parameters.
  Nucleic Acids Research, 2015 Jul 1; 43 (Web Server issue): W7-W14.; doi: 10.1093/nar/gkq443

  Landan, G., and D. Graur. (2008).
  Local reliability measures from sets of co-optimal multiple sequence alignments.
  Pac Symp Biocomput 13:15-24 [ABS] [PDF]

  When using the GUIDANCE algorithm please cite:
  Penn, O., Privman, E., Landan, G., Graur, D. and Pupko, T. (2010).
  An alignment confidence score capturing robustness to guide-tree uncertainty.
  Molecular Biology and Evolution, 2010 Aug;27(8):1759-67; doi:10.1093/molbev/msq066 [ABS] [PDF]

  When using the HoT algorithm please cite:
  Landan, G., and D. Graur. (2008).
  Local reliability measures from sets of co-optimal multiple sequence alignments.
  Pac Symp Biocomput 13:15-24 [ABS] [PDF]

• Pal2nal
  If you use PAL2NAL, please cite the following paper:
  Mikita Suyama, David Torrents, and Peer Bork (2006)
  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
  Nucleic Acids Res. 34, W609-W612.

• IQTree
  This One is a bit more complicated.

• Clustal Omega
  Citing Clustal
  Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, > Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence > alignments using Clustal Omega. Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75

• Biopython

• ETE

• PhyML

• Treelib?

• BioSQl?

Feel free to add more or the rest.

[grabear]

Stealing this. https://github.com/etetoolkit/ete/blob/master/ete3/citation.py