Cogent Usage Examples¶
A Note on the Computable Documentation¶
The following examples are all available as standalone text files which can be computed using the Python doctest module.
Data manipulation¶
- Translating DNA into protein
- Advanced sequence handling
- Complete version of manipulating sequence annotations
- Getting the reverse complement
- Map protein alignment gaps to DNA alignment gaps
- Creating and manipulating alignment profiles
- Compute the effect of a nucleotide substitution on residue polarity in two different genetic codes using GeneticCode and AAIndex
- Data Manipulation using
Table
- Working with macromolecular structures
- Selecting and grouping entities
- Querying NCBI for VWF
- Querying Ensembl
- Manipulation of Tree Node Objects
- An Example of Conditional Tree Node Modifications
Controlling 3rd party applications¶
General data analysis¶
Data Visualisation¶
Modelling Evolution¶
- The simplest script
- Performing a relative rate test
- A test of the neutral theory
- Allowing substitution model parameters to differ between branches
- Using codon models
- Use an empirical protein substitution model
- Likelihood analysis of multiple loci
- Reusing results to speed up optimisation
- Specifying and using an unrestricted nucleotide substitution model
- Simulate an alignment
- Performing a parametric bootstrap
- Estimate parameter values using a sampling from a dataset
- Perform a coevolutionary analysis on biological sequence alignments
- Analysis of rate heterogeneity
- Evaluate process heterogeneity using a Hidden Markov Model
- Seqsim Simple Alignment Simulation Example
- Seqsim Alignment Simulation Example with Non-standard alphabet
- Seqsim Simple Tree Simulation