USAGE:
Brief USAGE: ./progressivePIP [--local] [--SB] [--cross ] [--beta ] [--alpha ] [--gamma] [--pip] [--jc ] [--k80 ] [--hky85 ] [--mu ] [--lambda ] [--ancestral_seqs] [--all_trees] [-i ] [-I] [-M] [-m] [-a] [-C ] [-F] [--custom_model ] [--profile_out ] [-w] [-c ] [--early_refinement] [-W] ... [-r] ... [--custom_tr_cmd ] [--trd_output ] [--read_repeats ] [-R] ... [--repalign] [--repeat_indel_ext ] [--repeat_indel_rate ] [-A] [-P ] [-p ] [-D ] [-d ] [-x ] [-s ] [-l ] [-E ] [-e ] [-g ] [-f] [--aa] [--dna] [--codon] [--topology ] [-t ] [-O ] [-o ] [--] [--version] [-h]
Where:
--local use local/global tree
--SB stochastic backtracking
--cross cross sub-optimal solutions
--beta beta
--alpha alpha
--gamma use gamma distribution (4 classes)
--pip use PIP model of evolution
--jc rate
--k80 TsToTvRatio
--hky85 TsToTvRatio
--mu deletion rate
--lambda insertion rate
--ancestral_seqs output all ancestral sequences
--all_trees output all intermediate guide trees
-i , --iterations number of iterations re-estimating guide tree
-I, --input_order output sequences in input order (default: tree order)
-M, --mldist_gap use ML distances with gaps
-m, --mldist use ML distances
-a, --nwdist estimate initial distance tree from NW alignments
-C , --aafreqs_pseudocount pseudo-count for estimating equilibrium amino acid frequencies
-F, --estimate_aafreqs estimate equilibrium amino acid frequencies from input data
--custom_model custom substitution model in qmat format
--profile_out output ancestral sequence profiles
-w, --darwin use darwin's model of evolution (instead of WAG)
-c , --cs_profile library of context-sensitive profiles
--early_refinement perform early refinement
-W, --wls_refine (accepted multiple times) refine guide tree with weighted least-squares
-r, --reroot (accepted multiple times) reroot tree on all branches and minimize gap parsimony (specify twice for heuristic root search)
--custom_tr_cmd custom command for detecting tandem-repeats
--trd_output write TR detector output to file
--read_repeats read repeats from file
-R, --repeats (accepted multiple times) use T-Reks to identify tandem repeats
--repalign re-align detected tandem repeat units
--repeat_indel_ext repeat indel extension probability
--repeat_indel_rate insertion/deletion rate for repeat units (per site)
-A, --no_force_align do not force alignment of start/stop codons
-P , --max_pdist maximum p-distance (divergence) for alignment
-p , --min_pdist minimum p-distance (divergence) for alignment
-D , --max_dist maximum distance for alignment
-d , --min_dist minimum distance for alignment
-x , --cutoff_dist cutoff value for pairwise distance estimation
-s , --altsplice_prob alternative splicing probability
-l , --edge_halflife edge half-life
-E , --end_indel_prob probability of mismatching sequence ends (set to -1 to disable this feature)
-e , --gap_ext gap extension probability
-g , --indel_rate insertion/deletion rate
-f, --fasta output fasta format (instead of stockholm)
--aa align AA sequence
--dna align DNA sequence
--codon align DNA sequence based on a codon model
--topology topology of initial guide tree (branch lengths will be estimated)
-t , --tree initial guide tree
-O , --outputTreefile Output tree-file name
-o , --outputMSAfile Output MSA-file name
--, --ignore_rest Ignores the rest of the labeled arguments following this flag.
--version Displays version information and exits.
-h, --help Displays usage information and exits.
(required) input sequencesFor building progressivePIP from source you need: CMake >=2.8 (http://www.cmake.org) tclap >=1.1.0 (http://tclap.sourceforge.net) Eigen 2.0.x or 3.0.x (http://eigen.tuxfamily.org)
on Debian/Ubuntu you can install these programs/libraries with: sudo apt-get install cmake libtclap-dev libeigen2-dev
Then perform the following command to configure/build/install progressivePIP: cd BUILD ccmake .. (press "c" to configure and "g" to generate the Makefile, see below for additional configuration options) make progressivePIP make install
Additional CMake configuration options (in "ccmake .."):
EIGEN2_INCLUDE_DIR: set this to the path, where Eigen is installed, if you use Eigen 3.0.x or if Eigen has been installed at a non-default location (default location: /usr/include/eigen2)
WITH_EIGEN3: set this to ON, if you want to compile progressivePIP with Eigen 3.0.x
CMAKE_CXX_FLAGS: add options for the C++ compiler, like optimization flags, or additional search paths for include files (-I )
WITH_SSE: disable this option, if you build progressivePIP for a machine that does not support SSE2