AFLPM<scp>ax</scp>: a user‐friendly application for computing the optimal number of amplified fragment length polymorphism markers needed in phylogenetic reconstruction

Abstract Amplified fragment length polymorphisms (AFLPs) are widely used for phylogenetic inference especially in non‐model species. Frequently, trees obtained with other nuclear or mitochondrial markers or with morphological information need additional resolution, increased branch support, or independent data sources (i.e. unlinked loci). In such cases, the use of AFLPs is a quick and cheap option. Computer simulation has shown that dominant AFLP markers lead to less accurate tree topologies than bi‐allelic codominant markers such as SNPs, but this difference becomes negligible for shallow trees when using AFLP data sets that include a sufficiently large number of characters. Thus, determining how many AFLP characters are required to recover a given phylogeny is a key issue regarding the appropriateness of AFLPs for phylogenetic reconstruction. Here, we present a user‐friendly, java ‐based graphical interface, AFLPM ax , which executes an automatic pipeline of different programs providing the user with the optimal number of AFLP characters needed to recover a given phylogeny with high accuracy and support. Executables for Windows, linux and M ac OS X operating systems, source code and user manual are available from: http://webs.uvigo.es/acraaj/AFLPMax.htm .