Table 1 Features available in EggLib and alternative population genetics software packages
From: EggLib: processing, analysis and simulation tools for population genetics and genomics
EggLib | Biopython | PyCogent | Bio++ | DnaSP | ms | CoaSim | DiyABC | ABCToolbox | msABC | ABCreg | |
|---|---|---|---|---|---|---|---|---|---|---|---|
Reference | This paper | [4] | [17] | [18] | [19] | [20] | [21] | [22] | [23] | [24] | [25] |
Sequence data management | |||||||||||
Input format | FASTA + converters | Many formats | Many formats | Many formats | Several formats | Genepop format | Specific format | Tabular data | |||
Alignment | Available (wrappers) | Available (wrappers) | Available (wrappers) | ||||||||
Storage model | Full storage in memory | Full storage (alignments) and iterative parsing | Full storage in memory | Full storage in memory | Full storage in memory | ||||||
Sequence analysis | |||||||||||
BLAST wrapper | Available | Available | Available | ||||||||
Gene prediction | Available | ||||||||||
Diversity analysis | |||||||||||
Microsatellites | Built-in | Genepop wrapper | |||||||||
Sequences | Built-in | Built-in | Built-in | From simulations | |||||||
Coding sequences | With Bio++ | Built-in | |||||||||
Phylogenetics | Distance and maximum-likelihood methods through wrappers | Built-in distance and maximum likelihood methods + wrappers | Built-in distance and maximum likelihood methods | ||||||||
Simulations | |||||||||||
Coalescence (standard model) | Built-in and ms wrapper | ms wrapper | Available | Available | Available | - | |||||
Recombination | Available | Available | Available | Available | Available | ||||||
Structured models | Available | Available | Available | Available | |||||||
Diploid samples & selfing | Available | ||||||||||
Infinite-site model | Available | Available | Available | Fixed number of sites | |||||||
Homoplasy | Available | Available | Available | ||||||||
Microsatellite models | Available | Available | Available | ||||||||
Output | Sequences, FASTA, trees, statistics, Python objects | Arlequin-compatible file | P-values | Sequences, statistics | Sequences, Python objects | ||||||
ABC inference | |||||||||||
Models | Pre-defined models + all models allowed by the simulator (not restrictive) | Customizable divergence models with population size changes | Depends on the simulator used | All models allowed by ms | |||||||
Summary statistics | Pre-defined statistics sets + all statistics available in EggLib (not restrictive) | Microsatellite and within- and between-population sequence statistics | Calculated by simulator or provided by the user | Within- and between-population sequence statistics | |||||||
Analysis method | Rejection and local-linear regression | Rejection and local-linear regression | Rejection, local-linear regression, generalized linear models and others | Rejection and local-linear regression |