Added README

README

+#INSTALL:
+
+Phybema requires the installation of the following programms:
+
+  - python version >= 3.5
+  
+  - numpy
+  
+  - Java 1.7 (for TreeCmp)
+
+  Phybema contains the source code of the software TreeCmp.
+  The orginal source code can be found at https://eti.pg.edu.pl/treecmp/.
+  
+to compile Phybema call: 
+  
+    make
+    
+#TEST:
+
+to run the tests call:
+
+    make test
+  
+#CLEAN UP:
+
+    make clean
+  
+#RUN:
+
+run Phybema with:
+  
+          phybema.py [-h]
+          [--tools {andi,mash,...}
+          [{andi,mash,...} ...]]
+          [-o {pdf,png,svg,none}] [-d [metric [metric ...]]] [-m]
+          datasetpaths [datasetpaths ...]
+
+        positional arguments:
+          datasetpaths          Specify a list of paths to directories which 
+                                contain a datafile and optionally a reference
+                                tree. A datafile must be in 
+                                FASTA format (.fasta,.faa,.fna,.fasta.gz), 
+                                a reference tree must be 
+                                in newick format (.nh,.tre).
+                                All genomes must be contained in one FASTA file.
+                                For datafiles with a reference tree the 
+                                resulting NJ-tree (derived from the distances 
+                                delivered by the corresponding tool) will be 
+                                compared to the reference tree.
+                                The genome names will be cut after 10 characters. 
+                                The reference tree must contain the 
+                                exact genome names resulting.
+                                For datafiles without reference and if at least
+                                two tools have been specified, the resulting
+                                NJ-trees are compared against each other.
+
+        optional arguments:
+          -h, --help            show this help message and exit
+          --tools {andi,mash,...} 
+                  [{andi,mash,...} ...]
+                                Specify the tools to evaluate.
+                                If this is the last option, then use -- before
+                                specifying any data set.
+                                default: use all tools.
+          -o {pdf,png,svg,none}, --out_treefile_suffix {pdf,png,svg,none}
+                                Specify suffix of output files
+                                with the NJ-trees computed from the distance
+                                matrices delivered by each tool. The argument 
+                                "none" means that no graphic-file is 
+                                generated. This is useful for remote sessions, 
+                                where this does not work
+                                anyway, as the ete toolkit, which generates the
+                                graphics output requires Qt and an X-server
+                                default: pdf
+          -d [metric [metric ...]], --dist [metric [metric ...]]
+                                Specify the distance metrics to use for 
+                                comparing the resulting NJ-trees with the 
+                                reference tree.
+                                More than one metric is possible.
+                                Possible metrics are:
+                                ms	Matching Split metric
+                                pd	Path Difference metric
+                                qt	Quartet metric
+                                nrf	normalised Robinson-Foulds distance
+                                rf	Robinson-Foulds distance
+                                ms, pd, qt and rf are computed by TreeCmp,
+                                nrf is computed using the ETE3 toolkit
+                                default: use nrf only
+          -m, --mat             Write the distance matrices originally computed 
+                                by the different programs into out.
+
+#ADD A TOOL
+Technical Requirements for distance estimators
+• input: sequences in multi FASTA-Format
+• output: distance matrix in PHYLIP-format
+• output to file or stdout
+
+Add a new tool as an instance of the class DistanceEstimator in the 
+module estimators.py. Add your tool at the Point "ADD YOUR TOOL HERE".
+Include a tool by defining:
+
+        progname = DistanceEstimator(call,call_options,fixed_out_file_name,
+                   optional_end))
+
+  with:
+
+        progname                variable to add the defined instance 
+                                of DistanceEstimator
+
+        call                    Define the path to call the program from
+        
+        call_options            define program-specific options
+
+        fixed_out_file_name     if the output is written into a file:
+                                specify the name of the outputfile
+
+        optional_end            option to name parameters which have to be 
+                                defined at the end of a list of parameters 
+                                for calling the program.
+
+By adding progname into the list all_estimators the tool is added to phybema.
+
+#FOLDER STRUCTURE:
+
+  - src: includes scripts for Phybema
+  
+  - src_external: contains  the source code of the software TreeCmp.
+       The orginal source code can be found at https://eti.pg.edu.pl/treecmp/.
+  
+  - testdata: provides real and simulated data
+  
+  - testsiud: includes test scripts
+  
+  - temp: temporary files generated while calling Phybema will be written here
+  
+  - out: generated files will be written here
+  
+  Makefile
+  
+  README
+
+  
+
+
+  
+  

README.md

-# Phybema
-
-Sources and Data for the Phylogenetic Benchmarking Project Phybema