Hi, Any one have any idea about core genomic accumulation curve from the orthomcl output file?? My modified orthomcl output file looks something like: Gr1 Gr2 Gr3 Gr4 .............. row1 1 1 1 0 .............. row2 0 1 0 1 ............... row3 1 1 0 1 .............. ................... ................. from this file, I determine the pan genomic (total file as input) accumulation curve from the speccecum function of vegan as: mydata <- read.table('input_matrix_file.txt') sp <- specaccum(mydata, "random", permutations="100") But the problem I face is in determining core gene accumulation (rather depletion) curve (permutations of only 1-1 combinations) from this file. I could not find a way of doing it from this matrix file. I will be grateful if you anyone offer some advice to solve this problem. Thanks for your consideration. Utpal Bakshi -- output of sessionInfo(): R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] vegan_2.0-2 permute_0.6-2 loaded via a namespace (and not attached): [1] grid_2.13.1 lattice_0.19-30 -- Sent via the guest posting facility at bioconductor.org.