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User Manual - Emma Hodcroft

1. tree should be calculated A different length file will be output for each input tree and each collapsing threshold if appropriate Output is in a CSV comma delimited file with three columns corresponding to leaf name length from that leaf to the node previous to the root and average bootstrap value from that leaf to the root If the user has specified the rooting option r or rp the length and average bootstrap will be calculated after rooting Example java jar TreeCollapseCL jar b 0 5 p l t O f Sequences newick Will output files called sequences_05coll newick and Sequences_05coll csv r outgroupor rp outgroup optional Use this to specify that the tree should be rooted by the specified outgroup Out group can be specified by including the name of a single node or the name of a file that contains a list of the outgroup nodes one name per line no punctuation Specifying rp will root the tree and also output a Nexus Newick style copy of the rooted tree recommended whereas r will root the tree without any additional output Rooting is carried out before calculating length and other attributes and before collapsing if either of these is specified All input files in a run will be rooted by the same outgroup Example java jar TreeCollapseCL jar b 0 5 t O p rp G101360 f Sequences newick Will root by the node G1010360 and output files called Sequences_05coll newick and Sequences_root newick Con
2. TreeCollapseCL 3 2 i 7 Emma Hodcroft T Andrew Leigh Brown Group Institute of Evolutionary Biology University of Edinburgh 2012 This command line Java program takes in Nexus Newick style phylogenetic tree code that includes branch lengths and may include bootstrap values and analyses them using any combination of three main functions Rooting the tree Collapsing the tree Measuring the length and other attributes of the tree More details of these three functions are provided below The program output varies by the functions selected but trees are output in Nexus Newick style code and length attributes are output in a CSV comma delimited file 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 More details on the main three functions of the program Rooting the tree An outgroup is specified by the user and the tree is rooted or re rooted to that outgroup The rooting function behaves in the same way as the FigTree http tree bio ed ac uk software figtree program so that after rooting the branch length of the branch parental to the outgroup is split evenly between the outgroup and the rest of the tree and the new root node has no bootstrap value Collapsing th
3. antly slow down runtime and possibly even crash the run if turned on for very large files It is recommended that the user create a smaller test file if they wish to turn on the debug option Again it s probably not very useful Examples of program runs on the next page E Hodcroft 2012 TreeCollapseCL 3 2 Page 4 of 6 Examples of program runs These examples assume the user always wants to exclude decimal points p from output files and is always using the other file type t Change these settings as needed Remember that for input a directory d can be specified instead of a file multiple bootstraps can be used b 0 5 0 7 instead of just one b 0 5 output trees and a copy of the original tree can be returned without bootstrap values nbs and for an outgroup either a node name r G101360 or a file containing multiple node names r roots txt can be used To find length of a tree java jar TreeCollapseCL jar t O p 1 f Sequences newick To root the tree and print the rooted tree java jar TreeCollapseCL jar t O p rp roots txt f Sequences newick To root and find length java jar TreeCollapseCL jar t O p 1 r roots txt f Sequences newick To root find length and collapse java jar TreeCollapseCL jar b 0 5 t O p 1 r roots txt f Sequences newick To find length and collapse java jar TreeCollapseCL
4. ation or in Newick format without bootstrap values or with some nodes missing bootstrap values collapsing cannot be done if bootstrap values are not present Corrected errors in reading Nexus files Corrected errors in handling file names that included decimal points Updates since version 3 0 Now takes trees without bootstrap values or with some nodes missing bootstrap values collapsing cannot be done if bootstrap values are not present Can now correctly handle trees output from RAxML or other programs where an extra root branch length of 0 0 has been attached to the end of the code see parameter rax Stops the run and provides an error message with potential solutions if too much of the tree has been collapsed causing a recursive stack overflow E Hodcroft 2012 TreeCollapseCL 3 2 Page 6 of 6
5. e tree A threshold is provided by the user and all nodes with bootstrap values below this threshold are collapsed to polytomies Length of the tree is preserved Measuring length and other attributes The length from each leaf to the node above the root node if an outgroup is present the length from root to first node can be dictated more by the outgroup than anything else is calculated and the average bootstrap value average of each bootstrap value between the leaf node and the root is calculated for each leaf Updates since version 3 1 2 Previous updates on the last page Now compatible with Windows Shell auto glob when passing to specify file endings Removed outputting the level of a node when specifying the 1 parameter 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 Corrected error that assumed all files had a path before the file name caused a StringlndexOutofBoundsException Corrected a minor collapsing problem that caused slight under collapsing of some nodes Corrected rooting to be more robust with particular polytomies E Hodcroft 2012 TreeCollapseCL 3 2 Page 1 of 6 The parameters d or f MUST be supplied The parameters b 1 t p v
6. jar b 0 5 t O p 1 f Sequences newick To collapse only java jar TreeCollapseCL jar b 0 5 t O p f Sequences newick To root and collapse java jar TreeCollapseCL jar b 0 5 O p r roots txt f Sequences newick ct 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 In order for this to work correctly when specifying that length be calculated 1 your input files should all have a file ending that begins with n For this purpose newick nexus nex or even just n files will work Citation 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 TreeCollapseCL3 html E Hodcroft 2012 TreeCollapseCL 3 2 Page 5 of 6 Updates from Previous Versions Updates since version 3 1 1 Corrected file directory reading for Unix Linux Mac users Updates since version 3 1 Please read updated information on when and how to use rax and t Now takes trees with FigTree annot
7. o be used by putting them in parenthesis separated by commas no spaces Each tree will be run with all thresholds and output in a file that reflects the threshold used Example java jar TreeCollapseCL jar b 0 5 0 7 t O f Sequences newick Runs files at thresholds 0 5 and 0 7 will output files called Sequences_0 5coll newick and Sequences_0 7coll newick To force the filename to exclude the decimal point in decimal thresholds see p parameter t optional Use t to specify the file type that will be read in If this parameter is not given it defaults to o t O Default Use o capital o to specify that the file is the usual Newick Nexus type file with bootstrap values 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 E Hodcroft 2012 TreeCollapseCL 3 2 Page 2 of 6 d diror f file These specify the file use or directory use q of files to be read in Follow f with the file name Example java jar TreeCollapseCL jar b 0 5 t O f Sequences newick Foll
8. or rp are optional The parameter rax is now not needed and is depreciated nbs and r java jar TreeCollapseCL3 jar t d dir or f file b bootstrapThreshold r outgroup rp outgroup v L p nbs rax depreciated If the program is run without any parameters a list of parameters with descriptions is displayed A list of example runs using various combinations of the three main functions can be found at the end of this document as well as some tips on running multiple files and citation information Parameters b bootstrapThreshold optional Use p to indicate that you would like to collapse the tree by specifying the bootstrap threshold to be used to collapse the nodes Nodes at or below this threshold will be collapsed This will be done after rooting the tree if rooting has also been specified If calculating the length and other attributes has been specified specifying b will mean that level is included in the length file see 1 for more details p can be specified as a decimal or an integer depending on the type of bootstraps your file contains Example java jar TreeCollapseCL jar b 50 Sets threshold at 50 perhaps appropriate for bootstraps ranging from 0 to 100 Example java jar TreeCollapseCL jar b 0 5 Sets threshold at 0 5 perhaps appropriate for bootstraps ranging from 0 to 1 0 You can also specify a range of bootstrap thresholds t
9. ow d with the directory containing the files to be read in 3CD 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 TreeCollapseCL jar b 0 5 t O d C Users Bob Sequences Example java jar TreeCollapseCL jar b 0 5 t O 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 TreeCollapseCL jar b 0 5 t O d C Users Sequences newick Example java jar TreeCollapseCL jar b 0 5 t O d SCD nexus p optional Use this to specify that output file names should not include the decimal point in the decimal thresholds when multiple bootstrap thresholds are provided Example java jar TreeCollapseCL jar b 0 5 0 7 t O f Sequences newick Will output files called sequences_0 5coll newick and Sequences_0 7coll newick Example java jar TreeCollapseCL jar b 0 5 0 7 p t O f Sequences newick Will output files called Sequences_05coll newick and Sequences_07coll newick Using this parameter on integer thresholds will not change anything 1 optional Use this to specify that length and other attributes of the
10. tinued E Hodcroft 2012 TreeCollapseCL 3 2 Page 3 of 6 Example java jar TreeCollapseCL jar b 0 5 0 7 t O p 1 r roots txt f Sequences newick Will root by the node nodes listed in the file roots txt and output files called Sequences_05coll newick Sequences_07coll newick Sequences_O5coll csv and Sequences_07coll csv but no rooted tree file nbs optional Use this to specify that any output tree files should NOT contain bootstrap values The original tree will also be returned without bootstraps If collapsed or rooted trees are also being returned they will lack bootstrap values 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 TreeCollapseCL jar b 0 5 p nbs t O f Sequences newick Will output files called Sequences_05co11 newick and Sequences_nbs newick neither will contain bootstrap values rax depreciated This used to be required to specify the specific format of a Newick file The program now detects this automatically so this parameter is not needed anymore For backwards compatibility you can include it as a parameter but it will not affect the run 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 will signific

User Manual - Emma Hodcroft

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