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1. Maximum likelihood phylogenetic analysis using quartets and parallel computing Bioin formatics 18 502 504 Tamura K and Nei M 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees Mol Biol Evol 10 512 526 Tavar S 1986 Some probabilistic and statistical problems on the analysis of DNA se quences Lec Math Life Sci 17 57 86 Vinh L S and von Haeseler A 2004 IQPNNI Moving fast through tree space and stop ping in time Mol Biol Evol 21 1565 1571 Whelan S and Goldman N 2001 A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach Mol Biol Evol 18 691 699 Yang Z 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites Approximative methods J Mol Evol 39 306 314 Yang Z and Nielsen R 1998 Synonymous and nonsynonymous rate variation in nuclear genes of mammals J Mol Evol 46 409 418 Yang Z Nielsen R Goldman N and Pedersen A M K 2000 Codon substitution models for heterogeneous selection pressure at amino acid sites Genetics 155 431 449 182. 0 0410 0 0371 0 0091 0 0382 0 0495 0 0838 0 0246 0 0806 0 1011 0 0504 0 0220 0 0506 0 0431 0 0622 0 0543 0 0181 0 0307 0 0660 The format is following The first 19 lines describe the bellow triangle of the amino acid replacement matrix Then comes a list of 20 amino acid frequencies The rest of file will be ignored The order of amino acids is A R N D C Q E G H I L K M F P S T W Y V Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val 4 4 Other options Other options are easily to understand from the help dialog 5 Text menu options GENERAL OPTIONS Z Construct a sample tree by bootstrap o Display as outgroup n Minimum number of iterations s Stopping rule IQP OPTIONS p Probability of deleting a sequence k Number representatives SUBSTITUTION PROCESS d Type of sequence input data m Model of substitution t Ts Tv ratio 0 5 for JC69 f Base frequencies RATE HETEROGENEITY r Model of rate heterogeneity No FL 1 103 200 No stop after 200 iterations Nucleotides HKY85 Hasegawa et al 1985 Estimate from data Estimate from data Uniform rate quit q confirm y or change menu settings In the following the available options will be briefly introduced 5 1 General options e Option z Switch between reconstructing tree from the orignal alignment default or from a randomly resampled alignment using non parametric bootstrap e Option o Users ca
3. M 1992 The rapid generation of mutation data matrices from protein sequences Comput Appl Biosci 8 275 282 17 Jukes T H and Cantor C R 1969 Evolution of protein molecules In Munro H N ed Mammalian Protein Metabolism volume 3 pp 21 123 Academic Press New York Kimura M 1980 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences J Mol Evol 16 111 120 Meyer S and von Haeseler A 2003 Identifying site specific substitution rates Mol Biol Evol 20 182 189 Minh B Q Vinh L S von Haeseler A and Schmidt H A 2005 pIQPNNI parallel reconstruction of large maximum likelihood phylogenies Bioinformatics 21 3794 3796 Minh B Q Vinh L S Schmidt H A and von Haeseler A 2006 Large maximum likelihood trees In Proceedings of the 3rd NIC Symposium 2006 pp 357 365 Forschu nungszentrum J lich Germany M ller T and Vingron M 2000 Modeling amino acid replacement J Comput Biol 7 761 776 Nielsen R and Yang Z 1998 Likelihood models for detecting positively selected amino acid sites and applications to the HIV 1 envelope gene Genetics 148 929 936 Pedersen A K Wiuf C and Christiansen F B 1998 A codon based model designed to describe lentiviral evolution Mol Biol Evol 15 1069 1081 Schmidt H A Strimmer K Vingron M and von Haeseler A 2002 TREE PUZZLE
4. is the current version number and OS the operating system from http www cibiv at software iqpnni 2 Extract the files e g with tar xvzf iqpnni XXX OS tar gz under Unix This should create a directory iqpnni XXX 3 You will find the executable in iqpnni XXX src This executable you should rename to igpnni or iqpnni exe on Windows systems and copy it to your system s search path such that it is found by your system If you encounter problems please ask your local administrator for help 7 2 Sequential Version Source package To build IQPNNI from the sources you need a C compiler installed This is usually the case on UNIX Linux systems For Windows you might want to obtain CygWin MinWG MS Visual C or XCode for MacOSX Then you can follow the procedure below 1 Download the current version of the software iqpnni XXX tar gz or iqpnni XXX zip where XXX is the current version number from http www cibiv at software iqpnni 2 Extract the files e g with tar xvzf iqpnni XXX tar gz under Unix This should create a directory iqpnni XXX 3 Change into this directory 4 To compile the program type the following configure This should configure the package for the build You might also refer to the INSTALL file for more general details 13 make This compiles and builds the executable iqpnni or iqpnni exe on Windows systems to be found in the src directory This executable can copied to your system
5. 2 configure This should configure the package for the build using mpiCC as the C compiler You might also want to refer to the INSTALL file for more general details 14 make This compiles and builds the executable iqpnni or iqpnni exe on Windows systems to be found in the src directory This executable should be renamed to piqpnni and copied to your system s search path such that it is found by your system 5 To run the parallel version please refer to the documentation of your locally installed MPI implementation and or ask your local system administrator If you encounter problems please ask your local administrator for help 8 Version History Version 1 an oOo FP W WD Version o FP WwW N e 6 Version l 3 3 Resample the original alignment by bootstrap and construct the tree from the resampled alignment By default do not write treels file Use con to turn it on again Print site and pattern log likelihood with wsl and wpl option New prefix and param options Code cleanup Fix some important bugs incorrect master worker communication in parallel ver sion reported by Oliver Mirus nummerical overflow in stopping rule prediction vector overflow in ClusterArr class and others 3 2 Rewritten user manual Change number of iterations to minimum number of iterations Addtion of maximum number of iterations GTR model r
6. IQPNNI version 3 3 November 2008 Important Quartet Puzzling and Nearest Neighbor Interchange User Manual Please read carefully before using IQPNNI the first time Copyright C 2006 2009 by Bui Quang Minh Le Sy Vinh Heiko A Schmidt and Arndt von Haeseler Copyright C 2003 2005 by Le Sy Vinh and Arndt von Haeseler Bui Quang Minh Center for Integrative Bioinformatics Vienna Max F Perutz Laboratories Dr Bohr Gasse 9 6 A 1030 Vienna Austria email minh bui at mfpl ac at Heiko A Schmidt email heiko schmidt at mfpl ac at Arndt von Haeseler email arndt von haeseler at mfpl ac at Le Sy Vinh College of Technology Vietnam National University of Hanoi 144 Xuan Thuy Cau Giay Hanoi Vietnam License Agreement This program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 2 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WAR RANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details Contents 1 Introduction 2_Methods 3_ Main features 4 Command line options 4 1 General options o aaa 4 2 IQP options 4 3 Model options 4 3 1 Rate heterogeneity 4 3 2 User defined protei
7. TE Version 1 2 3 Scaling technique to avoid numerical underflow on large datasets It now can stably analyze alignments with more than 1 000 sequences At least twice faster than v3 0 The long double datatype is replaced by dou ble making it more compatible to most computers Memory consumption is reduced at least by half by a new mechanism of storing conditional likelihood vector New eigensystem adapted to reversible instantaneous rate matrix 3 0 betal The program now runs at least twice faster applying Newton s method instead of Brent s algorithm and some other algorithmic means Running in Parallel with Message Passing Interface MPI The option to change rate heterogeneity is now r instead of w The stopping rule is now switched off by default which can be changed using the s option 2 6 General Time Reversible model of evolution Site specific substitution rates Check point If the program was crashed or stopped by users it can continue from the last stopped point 16 Credits Some parts of the code were taken from TREE PUZZLE package Schmidt et al 2002 The source code to construct the BIONJ tree were taken from BIONJ software Gascuel 1997 Acknowledgement Financial support from the Wiener Wissenschafts Forschungs and Technologiefonds WWTF is greatly appreciated References Adachi J and Hasegawa M 1996 Model of amino acid substi
8. al Time Reversible e g For protein alignment e Dayhoff 1978 JTT 1999 vT 22000 mtREV 1996 WAG Boni rtREV 2002 BLOSUM62 1992 User defined protein model see Section 4 3 2 Note that the BLOSUM62 matrix should better not be used for phylogenetic reconstruction because it was constructed for database searches and does not reflect an evolutionary process For codon models e NY98 Nielsen and Yang 1998 Yang et al 2000 to infer positive selection Sub models include MO One ratio same as YN98 M1 Neutral Mla Nearly neutral M2 Selection M2a Positive selection M3 Discrete default model YN98 Yang and Nielsen 1998 special case of NY98 with 1 Ns Sy category GY94 Goldman and Yang 1994 CP98 Pedersen et al 1998 model incorporating CpG depression CGTR GTR version of nucleotide for codon unpublished 4 3 1 Rate heterogeneity The program can also assume rate heterogeneity Users can either choose uniform rate over all sites rate homogeneity default site specific substitution rates based on the model from Meyer and von Haeseler we Meyer and von Haeseler 2003 Gamma distributed rates or Gamma Invariable rates Note that rate heterogeneity is only allowed for DNA and protein data w rate_type e uniform the default homogeneous site rate model e gamma site rates follow a discrete gamma distribution Yang 1994 e igamma site rates
9. ates are scaled such that the rate from G to T is equal to 1 For G I model initialize proportion of invariable sites to the number of constant sites Check identical sequences 3 1 Codon model The program goes through two stages At first the tree is recon structed based on HKY model for DNA Then it applies codon model for inference of positively selected sites Gamma Invariable sites rate heterogeneity 15 Site specific rates Meyer and von Haeseler 2003 improved Also write out site rates based on empirical bayesian if gamma rate is specified New protein models rtREV Dimmic et al 2002 user defined model by a file containing amino acid replacement rates and frequencies 5 Warning if number of iterations is too small as recommended by the stopping rule 6 New command line options Version 1 Bugs fixed Zero state frequencies they are now replaced by a very small number Checkpoint now correctly recovered from stopped point Restriction on number of sites from limit 100 000 to unlimited now Bugs identified Parallel version on Infiniband system under MPICH 3 0 1 Zero iteration if user specifies number of iterations to be zero the program will only evaluate the starting tree either BIONJ or user defined tree by optimizing model paramters and branch lengths 2 Triplet tree the program can now run on alignment of just 3 sequences 6 Version 1 2 NO
10. ch among substitution models 10 The subsequent options depend on the type of data and model selected For DNA models the following options are available e Option f Users can specify the base frequencies or let the program estimate them from the input data Option t If HKY85 or TN93 model are chosen users can specify the transition transversion ratio between 0 2 and 32 0 or let the program estimate it from the input data de fault e Option uw For the TN93 model users can also enter the py pu ratio the ratio of pyrimidine transition rate to purine transition rate between 0 2 and 32 0 or let the program estimate it from the input data default e Option g If users choose GTR model they can specify six different rate parameters Transversion rate from A to C Transition rate from A to G Transversion rate from A to T Transversion rate from C to G Transition rate from C to T Transversion rate from G to T or let the program estimate them from the input data QANE For protein models e Option f Users can specify the amino acid frequencies from the default frequencies of the corresponding protein model or let the program estimate them from the input data For codon models e Option f Users can let the program estimate codon frequencies from the input data with one of following types Codon table default Equal F1x4 or F3x4 e Option t Users can sp
11. cify some options first with the command line and then change again using the text menu interface IQPNNI will start as follows First the input_file iqpnni checkpoint file is read if this file is available and the sfc option is NOT specified If the last run on this alignment was NOT finished the parameters recorded in the checkpoint file will be loaded and all the command line options will be omitted In this case you will see some printout like The program was not done from the last run Load parameters from the checkpoint file IQPNNI now displays the menu and waits for user input if option ni is not specified otherwise it starts the computation directly 4 1 General options n min_iterations and s stopping_rule These two options are not independent except you specify s off In any case IQPNNI will loop at least a number of min_iterations If you set s on the program will automatically estimate the number of iterations required to ensure that with a 95 confidence further search will not detect a better tree If you set s max max_iterations IQPNNI will always stop after max_iterations even if the stopping rule suggests more iterations By s max 0 it will set max_iterations to 10 times of min_iterations If n 0 is specified IQPNNI will only evaluate ML branch lengths of the starting tree either BioNJ tree or user tree no topology rearrangement is perform u user _
12. ecify the transition transversion ratio between 0 2 and 32 0 or let the program estimate it from the input data default e Option w If NY98 model is chosen users can specify the type of submodels see Section e Option g If NY98 model and Discrete submodel are chosen users can specify the number of Nonsynonymous Synonymous classes Default value is 3 11 5 4 Rate heterogeneity e Option r To switch among 3 types Uniform rate Gamma distributed rate and site specific rate Option a If users choose Gamma distributed rate they can specify the Gamma distribution shape parameter alpha between 0 1 and 100 0 or let IQPNNI program estimate it from the input data default e Option c If users choose Gamma distributed rates they can specify a number of Gamma rate categories between 2 and 32 The default is 4 e Option i To specify the proportion of invariable sites among No default Estimate from data or a user defined value 6 Output files Running results as well as input parameters are summarized in PREFIX iqpnni PREFIX is by default the input alignment file name However if prefix lt prefix_out gt option is specified PREFIX will be assigned with lt prefix_out gt Resulting tree will be written to PREFIX iqpnni treefile in Newick format If Gamma Gamma I or Meyer and von Haeseler s site specific model is used the rates for each alignment position will be wri
13. equential version Syntax iqpnni OPTIONS Filename GENERAL OPTIONS sn Se n lt min_iterations gt s lt stopping_rule gt u lt user_tree gt bs prefix lt prefix_out gt sfc ni IQP OPTIONS p lt probability gt k lt representatives gt MODEL OPTIONS m lt model gt Nucleotides Amino acids print this help dialog make the main loop to at least min_iterations either on off or max lt max_iterations gt defaut is off read the starting tree from user_tree file construct a bootstrap tree by resampling the alignment set prefix of output files default is aln name start from scratch don t load the check point file don t prompt for user option set the probability of deleting a sequence set the number of representatives set the model type for JC69 K2P F81 HKY85 TN93 GTR WAG Dayhoff JTT VT mtREV rtREV Blosum Protein coding DNA GY94 YN98 NY98 CP98 CGTR CPR Otherwise Name of file containing user protein model w lt rate_type gt c lt num_rate gt OTHER OPTIONS param lt pam_file gt seed lt number gt wsl wpl con either uniform gamma igamma or sitespec number of rate categories for gamma and igamma only use lt pam_file gt for parameter input instead of stdin set random number generator seed to lt number gt write site log likelihood to sitelh PHYLIP like write pattern log likelihood to patlh turn on writing treels off by default You can spe
14. follow a discrete gamma distribution plus one category of zero rate e sitespec site specific rates follow the model in Meyer and von Haeseler 2003 Note that for w sitespec option the tree is first reconstruced based on uniform rate model In the second phase this tree topology is used to infer site specific rates until convergence The procedure is described in Meyer and von Haeseler 2003 c num_rate The number of gamma rate categories if w gamma or w igamma is specifed Default value is 4 4 3 2 User defined protein model User defined protein model can be given with m filename An example file which defines the cpREV model Adachi et al 2000 is 105 227 357 175 43 4435 669 823 538 10 157 1745 768 400 10 499 152 1055 3691 10 3122 665 243 653 431 303 133 379 66 715 1405 331 441 1269 162 19 145 136 168 10 280 92 148 40 29 197 203 113 10 396 286 82 20 66 1745 236 4482 2430 412 48 3313 2629 263 305 345 218 185 125 61 47 159 202 113 21 10 1772 1351 193 68 53 97 22 726 10 145 25 127 454 1268 72 327 490 87 173 170 285 323 185 28 152 117 219 302 100 43 2440 385 2085 590 2331 396 568 691 303 216 516 868 93 487 1202 1340 314 1393 266 576 241 369 92 32 1040 156 918 645 148 260 2151 14 230 40 18 435 53 63 82 69 42 56 323 754 281 1466 391 142 10 1971 89 968 92 83 75 592 54 200 91 25 4797 159 10 86 468 49 73 29 189 247 215 2370 97 522 71 346 865 249 475 317 122 167 760 10 119 0 0755 0 0621
15. me filename bstrees NOTE Choose the option to build a consensus tree from puzzle menu sfc This tells the program not to load the checkpoint file to prevent IQPNNI from recovering from an interruption ni This is helpful to start a batch job The parameters will be displayed again but the program will not prompt for user input and just start the computation directly 4 2 IQP options p probability and k representatives These two options are concerned with the original IQP algorithm see Vinh and von Haeseler 2004 2005 for more details In short IQPNNI iterates through a number of steps to search the tree space In each step several taxa are randomly pruned away from the current best tree The proportion of deleted leaves is determined by the option p probability Then these leaves will be reinserted into the tree in a random order following the IQP algorithm which takes k representatives parameter into account This full tree will be rearranged according to the NNI algorithm resulting in an intermediate tree If this intermediate tree shows a better likelihood the current best tree will be updated This finishes one iteration of the IQPNNI algorithm 4 3 Model options m model For DNA alignment the following models are implemented e 3069 Jukes and Cantor 1969 K2P Kimura 1980 F81 Felsenstein 1981 HKY85 Hasegawa et al 1985 e TN93 Tamura and Nei 1993 e GTR Gener
16. n model 4 4 Other options 5 Text menu options ee ee ee A es Be Fe 5 4 Rate heterogeneity 6 Output files 7 Installation 7 1 Sequential Version Binary release 0 0 20 20200200000 7 2 Sequential Version Source package 0 00 0 0000 ee eee 8 7 3 Parallel Version Binary release 7 4 Parallel Version Source package Version History 10 10 10 12 12 13 13 13 14 14 15 1 Introduction IQPNNI is a computer program to reconstruct the evolutionary relationships among contem porary species based on DNA protein or protein coding sequences In case of protein coding sequences several codon models are implemented for inferring positive selection IQPNNI is a command line and menu driven program which allows users to specify the parameter values or let the program estimate them from the input data a nucleotide or amino acid alignment in PHYLIP format The options are classified into four main groups general options IQP options substitution process options and rate heterogeneity options IQPNNI is available free of charge from http www cibiv at software igqpnni IQPNNI is written in C It will run on most personal computers and workstations if compiled by a C compiler Please read the Installation section 7 for more details We suggest that this documentation should be read before using IQPNNI the first time To find out what s new in the current versi
17. n specify a sequence as the outgroup sequence The final tree with the highest likelihood will be rooted with respect to the outgroup sequence e Option n Users can specify the minimum number of iterations or use the default value e Option s Users can choose one of three possibilities to stop the program 1 The first possibility is s Stopping rule No stop after n iterations It means that the program will stop after n iterations 2 The second possibility is s Stopping rule if applicable Yes It means that the program will stop and output the optimal tree with 95 confi dence if at least three better trees found during the search otherwise it will stop after n iterations 3 The third possibility is s Stopping rule if applicable Yes and at most max iterations It is similar to the second possibility but the program will run at most max it erations 3 5 2 IQP options e Option p Users can specify the probability of deleting a sequence or let the program estimate it from the input data e Option k One can specify number of representatives leaves for a rooted tree However we strongly recommend to use the default value See Section 4 2 for more details of these parameters 5 3 Substitution process e Option d Users must specify the type of sequence input data Nucleotides Amino acids or Protein coding DNA e Option m To swit
18. on please read the Version History section 8 Important Notice In this new version 3 3 IQPNNI supports easier non parametric bootstrap see Section 4 1 and fixes some important bugs Therefore we strongly recommend you to download and install this new version Since version 3 2 the option Number of iterations is changed to Minimum number of iterations meaning that the program will run at least the specified number of iterations no matter if the stopping rule is applied or not This is to avoid the behavior that IQPNNI stops so early that does not guarantee to find a good tree Moreover another option with maximum number of iterations is also added to avoid cases where IQPNNI runs forever since the stopping rule suggest too many number of iterations For more details see Section 4 and 5 Since version 3 1 IQPNNI is extended to work on protein coding sequences In such cases it will first consider the data as DNA and reconstruct a tree based on the HKY85 model Then IQPNNI turns the alignment into codon frames and estimates codon model parameters based on the reconstructed tree Finally it infers sites under positive selection using Yang s empirical Bayesian method For more details see Section 8 2 Methods To cite the program please use the following papers e General method Vinh and von Haeseler 2004 IQPNNI Moving fast through tree space and stopping in time Mol Biol Evol 21 8 1565 1571 ht
19. s search path such that it is found by your system or it can be installed to the default destination e g usr local bin on UNIX Linux using make install If you encounter problems please ask your local administrator for help 7 3 Parallel Version Binary release There will be no binary version of the parallel program because it depends on the MPI library you have installed locally 7 4 Parallel Version Source package To build the MPI parallel version of IQPNNI pIQPNNI you need a functional C com piler installed This is usually the case on UNIX Linux systems For Windows you might want to obtain CygWin or XCode for MacOSX In addition you have to install an imple mentation of the MPI Message Passing Interface library There is a list of free imple mentations at http www lammpi org mpi implementations available Then you can follow the procedure below 1 Download the current version of the software iqpnni XXX tar gz or iqpnni XXX zip where XXX is the current version number from http www cibiv at software iqpnni 2 Extract the files e g with tar xvzf iqpnni XXX tar gz under Unix This should create a directory iqpnni XXX 3 Change into this directory 4 To compile the program you have to run the configure script with the environment variable CXX set to the MPI C compiler of your local MPI implementation and turn on the preprocessor directive PARALLEL e g env CXX mpiCC CXXFLAGS DPARALLEL 0
20. tp dx doi org 10 1093 molbev msh176dd e MPI parallelization Minh Vinh von Haeseler and Schmidt 2005 plIQPNNI parallel reconstruction of large maximum likelihood phylogenies Bioinformatics 21 19 3794 3796 http dx doi org 10 1093 bioinformatics bti594 e OpenMP and hybrid MPI OpenMP parallelization Minh Vinh Schmidt and von 2006 Large maximum likelihood trees In Proceedings of the 38rd NIC Sym posium 2006 pp 357 365 Forschunungszentrum J lich Germany http www fz juelich de nic series volume32 minh pdf e Inference of positive selection please cite this manual Main features e Reconstructing maximum likelihood tree on DNA or protein alignment e Supporting various substitution models for nucleotide amino acid and codon w o rate heterogeneity e NEW in ver 3 3 see Section 4 1 Resampling the alignment once by non parametric bootstrap and constructing an ML tree from the resampled alignment e Providing parallel version with MPI and OpenMP e Inferring positively selected sites on protein coding alignment e Inferring site specific rates under Gamma Gamma Invar or Meyer and von Haeseler model e Evaluating a user defined tree 4 Command line options Since version 3 0 users can specify parameters through a set of command line options which are extremely useful to start a batch job Run iqpnni h to print out a short description of available options WELCOME TO IQPNNI 3 3 s
21. tree Instead of starting the search from BioNJ tree IQPNNI will make use of the tree from user_tree file in Newick format The branch lengths of this tree will be ignored but the topology will be used to estimate the model parameters and also reestimate the branch lengths bs The orginal alignment will be randomly resampled once by non parametric bootstrap The tree will be reconstructed from this resampled alignment Note that this is NOT a full bootstrap analysis You will have to run IQPNNI n times with bs and prefix prefix_out see bellow to obtain n bootstrap trees Then use another program like TREE PUZZLE to construct a consensus tree from these n bootstrap trees prefix prefix_out All the output file names will apply this prefix_out instead of using the default alignment name for the prefix This option is very handy when combined with bs to construct several resampling trees from a bootstrap analysis so that the output files will not be overwritten Following is a small bash script under Linux to do a full bootstrap analysis using IQPNNI and TREE PUZZLE the script should be adapted before real usage bin bash n 100 filename alignment phy first run iqpnni n times for i 1 i lt n i do igpnni filename ni bs prefix bs i done concatenate all resulting trees into a big file cat bs treefile gt filename bstrees now call TREE PUZZLE to to construct a consensus tree puzzle consmrel filena
22. tten to PREFIX iqpnni rate IQPNNI will also create several files PREFIX iqpnni bionj BioNJ tree in Newick format PREFIX iqpnni treels List of all intermediate trees if option con is specified PREFIX iqpnni dist Maximum likelihood distance matrix based on the specified model in Phylip format PREFIX iqpnni sitelh Site likelihood if option ws1 is specified PREFIX iqpnni patlh Pattern frequency and likelihood if option wp1 is specified PREFIX iqpnni checkpoint program current parameters will be loaded in case of a crash or interruption PREFIX iqpnni prediction is used internally by the stopping rule This file is necessary for recovering from crash or interruption PREFIX iqpnni bootsample the bootstrap alignment resampled from the original align ment if option bs is specified This file is also necessary for recovering from crash or interruption 12 7 Installation See below for information how to install build the different versions of the IQPNNI software Executable versions of the sequential that is non parallel program are intended for a number of operating systems The parallel program pIQPNNI has to be built from the sources as it depends on the MPI library locally installed in your system 7 1 Sequential Version Binary release 1 You might want to download the executable version of IQPNNI for your operating system if it is available iqpnni XXX OS tar gz or iqpnni XXX OS zip where XXX
23. tution in proteins encoded by mitochondrial DNA J Mol Evol 42 459 468 Adachi J Waddell P J Martin W and Hasegawa M 2000 Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA J Mol Evol 50 348 358 Dayhoff M O Schwartz R M and Orcutt B C 1978 A model of evolutionary change in proteins In Dayhoff M O ed Atlas of Protein Sequence Structure volume 5 pp 345 352 National Biomedical Research Foundation Washington DC Dimmic M W Rest J S Mindell D P and Goldstein R A 2002 rtREV An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny J Mol Evol 55 65 73 Felsenstein J 1981 Evolutionary trees from DNA sequences a maximum likelihood ap proach J Mol Evol 17 368 376 Gascuel O 1997 BIONJ An improved version of the NJ algorithm based on a simple model of sequence data Mol Biol Evol 14 685 695 Goldman N and Yang Z 1994 A codon based model of nucleotide substitution for protein coding DNA sequences Mol Biol Evol 11 725 736 Hasegawa M Kishino H and Yano T A 1985 Dating of the human ape splitting by a molecular clock of mitochondrial DNA J Mol Evol 22 160 174 Henikoff S and Henikoff J G 1992 Amino acid substitution matrices from protein blocks Proc Natl Acad Sci USA 89 10915 10919 Jones D T Taylor W R and Thornton J
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