Table 1

Features available in EggLib and alternative population genetics software packages

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


De Mita and Siol BMC Genetics 2012 13:27   doi:10.1186/1471-2156-13-27

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