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datasnakes / OrthoEvolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
https://orthoevolution.readthedocs.io/en/master/
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Works Cited #21

Open grabear opened 7 years ago

grabear commented 7 years ago

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 commented 6 years ago

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

Feel free to add more or the rest.

grabear commented 6 years ago

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

  • [x] Biopython

  • [ ] ETE

  • [ ] PhyML

  • [ ] Treelib?

  • [ ] BioSQl?

Feel free to add more or the rest.

grabear commented 6 years ago

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

grabear commented 6 years ago

New way of adding references:

A new class has been designed to hold all of our info. Right now it's called "Webster". In the future we can add static YAML files to Manager/config/webster that will hold data that we regularly call. This will be particularly useful when using the YAML tagging for python objects and modules (#118). This will give us better readability as well as a better way to implement function dispatching.

GUIDANCE2:
  reference_1:
    citation: "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"
    link: "https://www.ncbi.nlm.nih.gov/pubmed/18229673"
    path: '!!python/object/apply:pkg_resources.resource_filename [Datasnakes.Manager.config.references, "GUIDANCE2_Accurate_Detection_of_Unreliable_Alignment_Regions_Accounting_for_the_Uncertainty_of_Multiple_Parameters.pdf"]'
  reference_2:
    citation: "Landan, G., and D. Graur. (2008).  Local Reliability Measures from Sets of Co-optimal
    Multiple Sequence Alignments.  Pac Symp Biocomput 13:15-24"
    link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489236/"
    path: '!!python/object/apply:pkg_resources.resource_filename [Datasnakes.Manager.config.references, "Local_Reliability_Measures_from_Sets_of_Co-optimal_Multiple_Sequence_Alignments.pdf"]'
PAL2NAL:
  reference_1:
    citation: "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."
    link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538804/"
    path: '!!python/object/apply:pkg_resources.resource_filename [Datasnakes.Manager.config.references, "PAL2NAL_ Robust_Conversion_of_Protein_Sequence_Alignments_into_the_Corresponding_Codon_Alignments.pdf]'
IQTREE:
  reference_1:
    citation: "LT Nguyen, H.A. Schmidt, A. von Haeseler, and BQ Minh (2015) IQ-TREE: A
    fast and effective stochastic algorithm for estimating maximum likelihood
    phylogenies. Mol. Biol. Evol., 32, 268-274."
    link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271533/"
    path: '!!python/object/apply:pkg_resources.resource_filename [Datasnakes.Manager.config.references, "IQ-TREE_A_Fast_and_Effective_Stochastic_Algorithm_for_Estimating_Maximum-Likelihood_Phylogenies.pdf"]'
CLUSTALO:
  reference_1:
    citation: "Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M,
    Söding J, Thompson JD, Higgins DG.  Fast, Scalable Generation of High-quality Protein Multiple Sequence
    Alignments Using Clustal Omega.  Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75."
    link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261699/"
    path: '!!python/object/apply:pkg_resources.resource_filename [Datasnakes.Manager.config.references, "Datasnakes/Manager/config/references/Fast_Scalable_Generation_of_High-Quality_Protein_Multiple_Sequence_Alignments_Using_Clustal_Omega.pdf"]'