PareTree 1.0.2 - Emma Hodcroft
Contents
1. java jar PareTree jar t O del Mouse_1990 d CD nexus del leavesToDelor keep leavesToKeep Use one or the other not both This parameter specifies the sequences that should be either deleted using de1 or kept using keep The user can specify either a single sequence name directly in the run command or specify a file that contains a list of sequences one per line no punctuation When using de1 all sequences in the file will be deleted When using keep all sequences not in the file will be deleted Any sequences in the file that are not in the tree will be ignored in both cases If you submit an empty file or a file where none of the sequences are in the tree using keep the program will terminate with an error If you submit just one sequence using keep the program will execute but many other programs will not accept the resulting single node tree The resulting tree will be written to a file with _pared added to the file name Example java jar PareTree jar keep goodSeqs txt t O f Sequences newick Will delete all sequences not in the file goodSeqs txt and output the resulting tree in Sequences_pared newick Example java jar PareTree jar del badSeqs txt t O f Sequences newick Will delete all sequences in the file badSegs txt and output the resulting tree in Sequences_pared newick Example java jar PareTree jar del Mouse_1990 t O f Seq2. for more details E Hodcroft 2013 PareTree 1 0 2 Page 1of5 Updates since version 1 0 1 Previous updates on last page topo can now be used to specify that output files should be written without branch lengths topology only Can be combined with nbs and de1 keep or used alone Now compatible with Windows Shell auto glob when passing to specify file endings t is now optional if not included the value defaults to o rax is now depreciated but can be included without affecting the run The program now automatically detects and handles a larger number of minor variations in format that can occur at the end of Newick files Parameter Notes The parameters d or MUST be supplied as well as del or keep and or nbs and or topo The parameters v and t are optional The parameter rax is now not needed and is depreciated java jar PareTree jar t d dir or f file del leavesToDelete keep leavesToKeep nbs topo v rax If the program is run without any parameters a list of parameters with descriptions is displayed Some tips on running multiple files can be found at the end of this document as well as citation information Parameters t optional Use t to specify the file type that will be read in t O Default Use o capital o to specify that the file is the usual Newick Nexus type file with bootstrap va
3. PareTree 1 0 2 Emma Hodcroft Andrew Leigh Brown Group Institute of Evolutionary Biology University of Edinburgh 2013 This command line Java program allows users to pare down their tree by either removing unwanted leaves tip nodes removing bootstrap information from the tree or removing branch lengths from the tree or any combination These functions can be accomplished in languages like R or Perl but Java allows very large trees to be pared down quickly efficiently and easily The program takes Nexus Newick style phylogenetic tree code as input that may or may not include bootstraps and outputs Newick style trees with the requested nodes and or bootstrap values removed Much like its sister program TreeCollapseCL this program accepts two types of file to see details on these types please see t below PLEASE NOTE am not responsible for any incorrect behaviour of this program do not guarantee that it will behave correctly or as you predict because cannot test it in every conceivable situation Reminder Deleting nodes from phylogenies is risky business Deleting nodes is unlikely to give you the same phylogeny as re running the tree with the corresponding sequences removed You could easily misrepresent your data to yourself and to others by deleting nodes to make a prettier picture Thus implore the user to run this program carefully and I do not condone it being used to intentionally misrepr
4. a 0 0458 144472 0 0118 144472 137802 0 0671 137802 Here leaf 121277 red has been deleted from the tree This lead to an internal node blue being deleted as well However the total distance from the root to all the other leaves remains unchanged The distance from 121277 s sister node 122448 to the next unaffected internal ancestral node purple also remains unchanged Tips on running multiple files If the user needs to run multiple files as input by specifying a directory d ensure they all have different names If they have been generated by a batch run or are otherwise likely to have similar names this program is designed to handle files that are numbered with the number in between decimal points preceding the file ending as shown SeqSet_run 1 newick SeqSet_run 2 newick This then allows you specify a directory where all files or all files with a specific ending will have the same sequences deleted as specified by del or keep or all have their bootstrap values removed Output files are modified so that the file name change is put before the number in the file ex SeqSet_run_pared 1 newick SeqSet_run_nbs 2 newick Example java jar PareTree jar t O del Mouse_1990 d C Users Sequences newick Example java jar PareTree jar t O nbs keep goodSeq txt d CD nexus Example java jar PareTree jar t O nbs topo d C Users Sequence
5. esent data Here are a few safer situations where this program might be useful Deleting identical sequences Some phylogenetic programs do not warn of identical sequences at the beginning of a run leading to leaf pairs with branch lengths of 0 Some programs have trouble with or will not accept branch lengths of 0 If the tree is large and the run takes many hours or days deleting the identical sequences and re running the tree or trees can be a very unappealing task Because both leaves have a branch length of 0 from the previous node deleting one will not affect the legitimacy of your tree and can save a lot of time Also the program can be put into a batch file or script so that the same sequences are deleted from many tree files quickly and easily Zooming In on Trees Simplifying Outgroups For display purposes PareTree could be used to delete all but a cluster of sequences from a tree allowing a better Zzoomed in image of a section of the tree the tree for easier examination Similarly if multiple monophyletic outgroup sequences have been used but are affecting the display of the tree all but one could be deleted and then this one renamed to reflect that it was originally a group of sequences It is worth mentioning that the total root to tip distance is kept the same for every leaf after other leaves are deleted Non deleted nodes will have the same total distance to the root as they did before See the page 4
6. lues preceding colons Unless the file was exported as Nexus with annotation in FigTree use this option or don t include the parameter at all Example B 0 04 C 0 03 0 83 0 01 Where 0 83 is the bootstrap value t F Use F to specify that the file is a Nexus type file that s been exported from FigTree with annotations These have bootstrap values within square brackets Example B 0 04 C 0 03 amp bs 0 83 0 01 Where 0 83 is the bootstrap value d diror f file These specify the file use or directory use d of files to be read in Follow f with the file name Example java jar PareTree jar t O del Mouse_1990 f Sequences newick Follow d with the directory containing the files to be read in sCD can be used as well If there may be spaces in folders or filenames in the path use double quotes to enclose the path It s a good idea to use these unless you re certain there are no spaces Example java jar PareTree jar t O del Mouse_1990 d C Users Bob Sequences Continued E Hodcroft 2013 PareTree 1 0 2 Page 2 of 5 Example java jar PareTree jar t O del Mouse_1990 d CD You can also specify the ending of the files to be read by using followed by the ending Be aware that this will only work on endings putting something before the will not work Example java jar PareTree jar t O del Mouse_1990 d C Users Sequences newick Example
7. s added to the name Example java jar PareTree jar topo t O f Sequences newick Will output a file called Sequences_topo newick which will not contain branch lengths Continued E Hodcroft 2013 PareTree 1 0 2 Page 3 of 5 Example java jar PareTree jar topo del badSeqs txt t O f Sequences newick Will delete all sequences in the file badSeqs txt and output the resulting tree in Sequences_pared newick without branch lengths v optional Use this to turn on very crude debug which will basically output intermediate flags and steps to the console It s probably not very useful and may slow down runtime and may possibly even crash the run if turned on for very large runs with large files Again it s probably not very useful rax depreciated This used to be required to specify the specific format of a Newick file The program now detects this automatically For backwards compatibility it can be included but it will not affect the run A Note on Branch Length Leaves remaining after deletion retain the same total distance from the root of the tree and from other internal ancestral nodes unaffected by the deletion This is done by adding the branch lengths of deleted internal nodes deleted because a leaf was deleted and there is no longer need for an internal bifurcation node are added to the branch lengths of remaining nodes For example 0 0703 0 0703 case 0 0703 122448 122448
8. s newick E Hodcroft 2013 PareTree 1 0 2 Page 4of5 Citation amp Feedback If you publish or present work that has been processed using this program please cite Emma Hodcroft and the website where this program can be downloaded http emmahodcroft com PareTree html If you have questions about using the program or would like to provide feedback or suggestions please use the Feedback page on my website http emmahodcroft com feedback html Updates from Previous Versions Updates since version 1 0 Corrected file directory reading for Unix Linux Mac users Corrected error that assumed all files had a path before the file name E Hodcroft 2013 PareTree 1 0 2 Page5of5
9. uences newick Will delete the sequence named Mouse_1990 and output the resulting tree in Sequences_pared newick nbs Use this to specify that any output tree files should NOT contain bootstrap values If del or keep has been used the resulting tree will automatically be returned without bootstrap values If they have not the original tree will be returned without bootstraps with _nbs added to the file name This can be useful if the user plans to use some functions in the R packages ape or MCMCg1mm as bootstrap information can cause some functions to work incorrectly Example java jar PareTree jar nbs t O f Sequences newick Will output a file called Sequences_nbs newick which will not contain bootstrap values Example java jar PareTree jar nbs del badSeqs txt t O f Sequences newick Will delete all sequences in the file oadSeqs txt and output the resulting tree in Sequences_pared newick without bootstrap values topo Use this to specify that any output tree files should NOT contain branch lengths that it should be a topology only If del or keep has been used the resulting tree will automatically be returned without branch lengths If they have not the original tree will be returned without branch lengths with _topo added to the file name If nbs has been used it will be returned without branch lengths and without bootstrap values with _nb
Download Pdf Manuals
Related Search