Script started on Wed 29 Jun 2016 09:03:32 PM EDT ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ R R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: i686-pc-linux-gnu (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("ape") > library("seqinr") Loading required package: ade4 Attaching package: ‘seqinr’ The following objects are masked from ‘package:ape’: as.alignment, consensus > > # input seq names > wg_seqs <- c("EF013666", "EF013665", "EF013775", "EF013664", "EF013669", "AY867423", "EF013671", "AY867427", "EF013690", "AY703626", "EF0 13663", "EF013661", "AY867421", "AY867429", "AY703634", "EF013660") > # read from GenBank > wg <- read.GenBank(wg_seqs, species.names=T) > # check the species names > attr(wg, "species") [1] "Aenictus_ceylonicus" [2] "Aenictogiton_sp._ZAM02" [3] "Tatuidris_sp._ECU01" [4] "Adetomyrma_sp._MAD02" [5] "Aneuretus_simoni" [6] "Acanthostichus_kirbyi" [7] "Anonychomyrma_gilberti" [8] "Dorylus_helvolus" [9] "Cheliomyrmex_cf._morosus_CASENT0007006" [10] "Ectatomma_opaciventre" [11] "Acropyga_acutiventris" [12] "Acanthoponera_minor" [13] "Leptanilla_sp._D233" [14] "Leptanilloides_mckennae" [15] "Myrmecia_pyriformis_Smith,_1858" [16] "Acanthognathus_ocellatus" > > lr_seqs <- c("EF013538", "EF013537", "EF013647", "EF013536", "EF013541", "AY867485", "EF013543", "AY867489", "EF013562", "AY703760", "EF0 13535", "EF013533", "AY867483", "AY867491", "AY703768", "EF013532") > lr <- read.GenBank(lr_seqs, species.names=T) > # make sure the names are the same > attr(lr, "species") [1] "Aenictus_ceylonicus" [2] "Aenictogiton_sp._ZAM02" [3] "Tatuidris_sp._ECU01" [4] "Adetomyrma_sp._MAD02" [5] "Aneuretus_simoni" [6] "Acanthostichus_kirbyi" [7] "Anonychomyrma_gilberti" [8] "Dorylus_helvolus" [9] "Cheliomyrmex_cf._morosus_CASENT0007006" [10] "Ectatomma_opaciventre" [11] "Acropyga_acutiventris" [12] "Acanthoponera_minor" [13] "Leptanilla_sp._D233" [14] "Leptanilloides_mckennae" [15] "Myrmecia_pyriformis_Smith,_1858" [16] "Acanthognathus_ocellatus" > > # write the files preserving names > write.fasta(wg, names=attr(wg, "species"), file.out="wingless.fas") > write.fasta(lr, names=attr(lr, "species"), file.out="LWRh.fas") > > quit() Save workspace image? [y/n/c]: n ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ mafft wingless.fas > wingless_aln.fas nseq = 16 distance = ktuples iterate = 0 cycle = 2 nthread = 0 generating 200PAM scoring matrix for nucleotides ... done done done scoremtx = -1 Gap Penalty = -1.53, +0.00, +0.00 tuplesize = 6, dorp = d Making a distance matrix .. WARNING : 2 unknown characters 1 / 16 11 / 16 done. Constructing a UPGMA tree ... 0 / 16 10 / 16 done. Progressive alignment ... STEP 1 / 15 f STEP 2 / 15 f STEP 3 / 15 f STEP 4 / 15 f STEP 5 / 15 f STEP 6 / 15 f STEP 7 / 15 f STEP 8 / 15 f STEP 9 / 15 f STEP 10 / 15 d STEP 11 / 15 d STEP 12 / 15 d STEP 13 / 15 d STEP 14 / 15 d STEP 15 / 15 d done. disttbfast (nuc) Version 7.123b alg=A, model=DNA200 (2), 1.530 ( 4.590), -0.000 (-0.000) 0 thread(s) nthread = 0 blosum 62 / kimura 200 generating 200PAM scoring matrix for nucleotides ... done done done scoremtx = -1 Gap Penalty = -1.53, +0.00, +0.00 Making a distance matrix .. 0 / 15 10 / 15 done. Constructing a UPGMA tree ... 0 / 16 10 / 16 done. Progressive alignment ... STEP 1 /15 f STEP 2 /15 f STEP 3 /15 f STEP 4 /15 f STEP 5 /15 f STEP 6 /15 f STEP 7 /15 f STEP 8 /15 f STEP 9 /15 f STEP 10 /15 d STEP 11 /15 d STEP 12 /15 d STEP 13 /15 d STEP 14 /15 d STEP 15 /15 d done. tbfast (nuc) Version 7.123b alg=A, model=DNA200 (2), 1.530 ( 4.590), -0.000 (-0.000) 0 thread(s) Strategy: FFT-NS-2 (Fast but rough) Progressive method (guide trees were built 2 times.) If unsure which option to use, try 'mafft --auto input > output'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. The default gap scoring scheme has been changed in version 7.110 (2013 Oct). It tends to insert more gaps into gap-rich regions than previous versions. To disable this change, add the --legacygappenalty option. ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ mafft LWRh.fas > LWRh_aln.fas nseq = 16 distance = ktuples iterate = 0 cycle = 2 nthread = 0 generating 200PAM scoring matrix for nucleotides ... done done done scoremtx = -1 Gap Penalty = -1.53, +0.00, +0.00 tuplesize = 6, dorp = d Making a distance matrix .. 1 / 16 11 / 16 done. Constructing a UPGMA tree ... 0 / 16 10 / 16 done. Progressive alignment ... STEP 1 / 15 f STEP 2 / 15 f STEP 3 / 15 f STEP 4 / 15 f STEP 5 / 15 f STEP 6 / 15 f STEP 7 / 15 f STEP 8 / 15 f STEP 9 / 15 f STEP 10 / 15 f STEP 11 / 15 d STEP 12 / 15 d STEP 13 / 15 d Reallocating..done. *alloclen = 2149 STEP 14 / 15 d STEP 15 / 15 d done. disttbfast (nuc) Version 7.123b alg=A, model=DNA200 (2), 1.530 ( 4.590), -0.000 (-0.000) 0 thread(s) nthread = 0 blosum 62 / kimura 200 generating 200PAM scoring matrix for nucleotides ... done done done scoremtx = -1 Gap Penalty = -1.53, +0.00, +0.00 Making a distance matrix .. 0 / 15 10 / 15 done. Constructing a UPGMA tree ... 0 / 16 10 / 16 done. Progressive alignment ... STEP 1 /15 f STEP 2 /15 f STEP 3 /15 f STEP 4 /15 f STEP 5 /15 f STEP 6 /15 f STEP 7 /15 f STEP 8 /15 f STEP 9 /15 f STEP 10 /15 d STEP 11 /15 d STEP 12 /15 d STEP 13 /15 d STEP 14 /15 d STEP 15 /15 d done. tbfast (nuc) Version 7.123b alg=A, model=DNA200 (2), 1.530 ( 4.590), -0.000 (-0.000) 0 thread(s) Strategy: FFT-NS-2 (Fast but rough) Progressive method (guide trees were built 2 times.) If unsure which option to use, try 'mafft --auto input > output'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. The default gap scoring scheme has been changed in version 7.110 (2013 Oct). It tends to insert more gaps into gap-rich regions than previous versions. To disable this change, add the --legacygappenalty option. ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ amas concat -i *aln.fas -d dna -f fasta --out-format phylip Wrote concatenated sequences to phylip file 'concatenated.out' Wrote partitions for the concatenated file to 'partitions.txt' ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ sed -i 's/,//g' concatenated.out ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ sed -i 's/\.//g' concatenated.out ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ raxml -T 2 -d -m GTRGAMMA -p 1234 -s concatenated.out -o Leptanilla_sp_D233 -n test1 Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" This is the RAxML Master Pthread This is RAxML Worker Pthread Number: 1 This is RAxML version 8.1.22 released by Alexandros Stamatakis on June 15 2015. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Alignment has 538 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 6.44% RAxML rapid hill-climbing mode Using 1 distinct models/data partitions with joint branch length optimization Executing 1 inferences on the original alignment using 1 distinct complete random trees All free model parameters will be estimated by RAxML GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units Partition: 0 Alignment Patterns: 538 Name: No Name Provided DataType: DNA Substitution Matrix: GTR RAxML was called as follows: raxml -T 2 -d -m GTRGAMMA -p 1234 -s concatenated.out -o Leptanilla_sp_D233 -n test1 Partition: 0 with name: No Name Provided Base frequencies: 0.228 0.277 0.254 0.241 Inference[0]: Time 3.294494 GAMMA-based likelihood -8195.674749, best rearrangement setting 5 Conducting final model optimizations on all 1 trees under GAMMA-based models .... Inference[0] final GAMMA-based Likelihood: -8193.002812 tree written to file /home/mlb/Dropbox/script_test/RAxML_result.test1 Starting final GAMMA-based thorough Optimization on tree 0 likelihood -8193.002812 .... Final GAMMA-based Score of best tree -8193.002812 Program execution info written to /home/mlb/Dropbox/script_test/RAxML_info.test1 Best-scoring ML tree written to: /home/mlb/Dropbox/script_test/RAxML_bestTree.test1 Overall execution time: 4.558747 secs or 0.001266 hours or 0.000053 days ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ python Python 2.7.6 (default, Mar 22 2014, 22:59:38) [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import dendropy >>> >>> tree = dendropy.Tree.get_from_path("RAxML_bestTree.test1", "newick") >>> print(tree.as_ascii_plot()) /------------ Leptanilloides mckennae /------------------------------------+ | \------------ Cheliomyrmex cf morosus CASENT0007006 | /-------------------------------------+ /------------ Dorylus helvolus | | /-----------+ | | /------------+ \------------ Aenictogiton sp ZAM02 | | | | | \-----------+ \------------------------ Aenictus ceylonicus | | | \------------------------------------- Acanthostichus kirbyi | | /-------------------------------------------------------------- Anonychomyrma gilberti /-----------+ | | | | /------------------------ Aneuretus simoni | | | /------------+ | | | | | /------------ Adetomyrma sp MAD02 | | /-----------+ | \-----------+ | | | | /-----------+ \------------ Tatuidris sp ECU01 | | | | | | | | | | | | /------------------------ Acanthognathus ocellatus + | | | | \------------+ | \------------+ \------------+ | /------------ Acanthoponera minor | | | \-----------+ | | | \------------ Ectatomma opaciventre | | | | | \------------------------------------------------- Acropyga acutiventris | | | \-------------------------------------------------------------------------- Myrmecia pyriformis Smith 1858 | \--------------------------------------------------------------------------------------------------- Leptanilla sp D233 >>> quit() ]0;mlb@mlb-VirtualBox: ~/Dropbox/script_testmlb@mlb-VirtualBox:~/Dropbox/script_test$ exit exit Script done on Wed 29 Jun 2016 09:05:13 PM EDT