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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        
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