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Table 1 Overview of the evaluated tools

From: Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies

Tool t RAM ts. rep. m/w Description Input Output lang. Reference
χ 2 6 s 221 M No No +/+ Pearson χ2 test for homogeneity (vectorized implementation) freq, cov, Ne p R [14]
E&R- χ2 8 s 306 M Yes No +/+ χ2 test adapted to account for drift freq, cov, Ne p R [12]
CLEAR 3000 s 1100 M Yes Yes +/+ Discrete HMM of allele trajectories under a WF model sync,Ne s, Ne, h, LL Python [11]
cmh 216 s 145 M No Yes +/+ Test for homogeneity (similar to χ2) accounting for stratified data sync p Perl/R [13]
E&R-cmh 8 s 560 M Yes Yes +/+ CMH test adapted to account for drift freq, cov, Ne p R [12]
LLS 1091 s (83 h) 340 M Yes Yes +/+ Linear model with least square regression of logit-transformed allele frequencies freq, cov, Ne p, s, h R [14]
LRT-1 31 s 127 M No Yes −/− LRT of parallel selection freq, cov, Ne LRT, \(\hat \delta \) Python [15]
LRT-2 31 s 127 M No Yes −/− LRT of heterogeneous selection freq, cov, Ne LRT, dxr Python [15]
GLM 220 s 300 M Yes Yes +/+ Quasibinomial GLM with replicates and time as predictors freq p R [16]
LM 157 s 300 M Yes Yes +/+ LM with replicates and time as predictors freq p R [16]
BBGP 37 h 15 M Yes Yes +/+ A Bayesian model of allele trajectories following a Gaussian process sync BF R [17]
FIT1 16 s 220 M Yes No −/− A t test with allele trajectories modeled as a Brownian process freq p R [18]
FIT2 68 s 220 M No Yes −/− A t test with allele frequencies differences between two time points freq p R [18]
WFABC 42 h 8 MB Yes No +/+ ABC of WF dynamics with selection freq, Ne (h) BF, s C++ [20]
slattice 41 h 250 M Yes No +/+ HMM of allele trajectories under a WF model using an EM algorithm freq, Ne (h) s, LL R [19]
  1. For each tool, we show the time required to analyze a small data set (t, either in seconds (s) or hours (h)), the memory requirements (RAM), if time series data may be used (ts.), if replicates are accepted (rep), if a manual and a walk-through is available (m/w), a short description, the required input, the generated output, the programming language (lang.), and the reference for LLS the time required to estimate the selection coefficient and the p-value (in brackets) is provided. sync file, freq allele frequency, cov coverage, Ne effective population size, h heterozygous effect, p value, s selection coefficient, LRT likelihood ratio test, BF Bayes factor, LL log-likelihood, \(\hat \delta \) shared allele frequency change, dxr change in allele frequency in a single replicate r