User Manual - Indian Institute of Technology Kharagpur
Contents
1. OK K K K K K K 2K K 3K K 3K 2K K 2K 2 3K 2K 3K K K K 2s 3K 2K 3K K 3K 2k K 2k K 2k Introduction 9K KO OO OO EK COSPEDTree is a python based tool for computing supertree from input candidate source trees Supertree computation is formed using a greedy approach of partitioning the input set of taxa based on equivalence relation The relationship among a set of taxa is determined by ancestor descendent sibling no relation characteristics Based on such equivalence partitioning a Directed Acyclic Graph DAG is formed initially from which the output tree is generated Input source trees can be either in NEWICK format or in NEXUS format However all the source trees should have identical input formats Output tree is generated in the NEWICK format SEC 2 9 C2 ooo o 9 o a ak Ka 2 k aK a k k k k k Dependencies OK K K K K 2K K 2K K 3K 2K 3K 2K K 2K K 3K 2K 3K K K 2K 2s 3K 2K 3K K K 2k K 2k K 2k COSPEDTree is developed in Linux Systems Ubuntu 12 04 using Python 2 7 If a system alreay has python installed and the package has version lower than 2 7 then there can be problems as tested So in such case corresponding package upgrade is requested The executable is tested with different versions of Ubuntu For systems having Ubuntu with lower versions please notify in case of any errors The executable does not require any libraries to be installed prior execution aooaa oao oo o o o k k ok k k k ae k k Execution ok 22. d with the product of priority metric and the frequency associated with corresponding relation between concerned taxa pair Subsequently iterations are carried out with the score metric values 3 p option is for specifying the input tree format as denoted by inp_file format if input file contains the trees in NEWICK format then specify the option as p 1 1 stands for newick if input file contains the trees in NEXUS format then specify the option as p 2 2 stands for nexus 4 q option is for specifying the number of priority queues by no_of_queues employed for storing and manipulation of the score metric if number of queues is 1 Q_ one in the manuscript then specify the option as q 1 if number of queues is 2 Q_ two in the manuscript then specify the option as q 2 aooaa ooo o k 2 k k a k a k k k FINAL OUTPUT SUPERTREE OK K K K K K K 2K K 3K 2K 3K K K 2K 3K 3K 2K 3K K 3K ok In the same directory containing the source trees as specified by source_tree_input_ filename upon execution of above command one folder will be created as per the following naming convention inpfilefmt_ I _costupdate_ c _no_of_queue_ q include all_multi_reln_ a Here I corresponds to the value of input file format It is 1 or 2 c is False since dynamic cost update is disabled q is the number of queues It will be 1 or 2 a is False Within the folder two text files will be created 1 comple
3. g Indian Institute of Technology Kharagpur lt sourya bhatta gmail com gt
4. of i 2k of K ok K K of k ok of kK ok kK k of k Kk Kk K kK Kk ok K K ok K COSPEDTree is provided as a stand along executable The executable contains binaries of the source codes and the used libraries static libraries COSPEDTree is to be executed with the following command line options from a terminal assuming the present working directory contains the executable COSPEDTree options OK K K K 3K 2K K 3K 2K 3K K 3K os K 3K 2K 3K FK K ok 2k NOTE All the options except the first three signify toggle complement of their corresponding DEFAULT values First option help displays these command line parameters It Is Preferable For A Beginner To Not Use Any Option Other Than The Second And Third Options Second option is for specifying the input filename mandatory Third option is for specifying the corresponding file format mandatory for nexus file format data OK K K K K K K 2K K 3K K 3K 2K K 2K K 3K K 3K 2K K ok 3K Details of the options are mentioned below h help show this help message and exit I INP_FILENAME INPFILE INP_FILENAME name of the input file containing candidate source trees p INP_FILE_FORMAT inpform INP_FILE FORMAT 1 default input file format is NEWICK 2 input file format is NEXUS q NO_OF QUEUES queues NO_OF QUEUES 1 only a single max priority queue is used for storing the score metrics 2 default two separate queues are used to store the conflicting and non conflicting ta
5. ost assignment at the beginning to all the edges subsequently no update of edge costs is performed and edge selection is carried out with the initial cost settings Default FALSE f fractwt if true this option uses fractional values of edge weights for cost updation and edge selection Default FALSE aooaa oo k a a ae k ak k k k EXAMPLE OF COMMANDS OK K K K K K K 2K K 3K 2K 3K K K 2K K 3K ok 3K OK K K K K K K 2K K 3K ik K 2K K 3K 3K 3K is K 2K K 3K 2K 3K K K K K 3K K 3K K K K 3K 3K 2K 3K 2K K gt K 3K CASE A when user makes dynamic scoring OFF only static initialized score values are used for supertree construction corresponding results are provdided in the manuscript COuplet Supertree by Equivalence Partitioning of taxa set and DAG formation Sourya Bhattacharyya and Jayanta Mukhopadhyay Proceedings of 5th ACM Conference on Bioinformatics Computational Biology and Health Informatics ACM BCB Newport California September 2014 pp 259 268 SR IE 21 9 E22 2 9 E E 2 2 a a a a ae ok a a 2 COSPEDTree I source_tree_input_filename c p inp_file_format q no_of_queues command descriptions 1 Using I command we specify the input filename denoted by source_tree_input_ filename Replace the filename with the full or relative path of custom input file containing the source trees 2 c option is to disable the updation of the score metric values at each iteration Score metric values are initialize
6. te_output_description txt containing the details of execution output supertree and performance metric values with respect to sumFP sumFN and sumRF 2 Text file output_supertree_newick tre which contains the derived supertree in both newick string representation as well as a tree plot The tree can be used subsequently for performance metric computation 3K K K K K K K 2K K 3K K K 2K K 2K 2K 3K K K 2s K 3K 2K 3K is K 2K K 3K 2K 3K K K ois 2K 3K 2K 3K K K ok 2 CASE B when user makes dynamic scoring ON corresponding results are provdided in the manuscript COSPEDTree COuplet Supertree by Equivalence Partitioning of taxa set and DAG formation Sourya Bhattacharyya and Jayanta Mukherjee accepted for publication in IEEE ACM Transaction on Computational Biology and Bioinformatics OK K K K K K K 2K K 3K 2K K Ik K 2K 2K 3K K K 2K K 3K 2K 3K K K 2K K 3K 2K 3K 2s K 2K 3K 3K 2K 3K 2K K K 3K COSPEDTree I source_tree_input filename p inp_file_format q no_of_queues Here there is no c option thus enabling the cost update option Note cost update operation is time consuming So users are advised to rather use the earlier command line option Details of output files are same as above SE 21 9 C2 ooo a o 9 9 k k 2 k k k k k k k For any queries please contact 3K K K K K 2K K 2K K 3K 2K 3K K K 2K K 3K 2K 3K K K 2K K 3K 2K 3K K K 2K 2K 3K K 3K Sourya Bhattacharyya Department of Computer Science and Engineerin
7. xa pairs and corresponding score metrics a all if True then for conflicting taxa pairs at least two relations between them are supported by the source trees all possible four relations between them are considered and included in the score metric priority queue Otherwise if it is False information for only the relations which are supported by the source trees are included in the score metric priority queue Default FALSE n preservenoedge if true then it prioritizes NO edge type once an edge is marked as NO RELATION edge it will not be changed Default TRUE e equivpart if true then it clusters a group of taxa on the basis of equivalence partition Default TRUE r rooted if true then trees are read and processed as rooted trees Default FALSE u underscore if true then this option preserves the underscores of the names of taxa Default TRUE c costupdate if true then this option updates the edge costs during each iteration of edge connectivity Default TRUE s singleedgepriority if true then this option connects two taxa in the final supertree if those two taxa have only one single relation in the source trees that is non conflicting taxa pairs are separated first Default TRUE t tiecase if true then during selection among multiple edges having equal cost this option prioritizes certain edge types Default TRUE 1 initcost if true then this option uses one single edge c
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