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Bootstrap replicates were obtained by sampling with replacement within age/cohort group cells.

For ML, which is much more computer intensive, 100 bootstrap replicates were obtained.

Bootstrap replicates were obtained by randomly sampling with replacement within age/cohort group cells.

All parameters were optimized and 1002 bootstrap replicates were obtained from the tree (commands: mpirun -n 6 phyml-mpi -i 175toPhyML.phylip -b 1002 -d aa -m LG -f m -s SPR --rand_start --n_rand_starts 5 -v e -a e -o tlr).

Maximum Parsimony trees and bootstrap replicates were obtained using SEQBOOT, PROTPARS and CONSENSE and Maximum Likelihood trees were inferred using PROML from the PHYLIP package using the default settings [ 79].

Maximum-likelihood (ML), neighbor-joining (NJ), and maximum-parsimony (MP) phylogenetic trees were generated using MEGA 6 software [ 15]; 1000 bootstrap replicates were obtained in the NJ and MP analysis.

To assess the reliability of the nodes, 1000 bootstrap replicates were obtained with the program SEQBOOT within the PHYLIP [ 29] and analysed with the program DNAML under the multiple dataset option.

Neighbor-joining bootstrap values (10,000 replicates) were obtained in MEGA4 [ 57].

Majority-rule consensus trees of 100 bootstrap replicates were also obtained from maximum likelihood (ML) phylogenies obtained using the JTT model plus a gamma rate distribution approximated using 5 categories.

In none of the bootstrap replicates was monophyly of Netrin obtained.

And third, if a bootstrap is applied, which number of bootstrap replicates is required to obtain a sufficiently stable estimate of the desired quantile for the H 0 case (Results, Section 4.3)?