### CompareToBootstrap.pl Usage Example Source: https://github.com/morgannprice/fasttree/blob/main/treecmp.txt Compares a main tree to bootstrapped trees and outputs a new tree with bootstrap values as internal node names. Input trees must be in Newick format. ```bash CompareToBootstrap.pl -tree main_tree -boot bootstrapped_trees > new_tree ``` ```bash CompareToBootstrap main_tree bootstrapped_trees > new_tree ``` -------------------------------- ### Fasta Format Example Source: https://github.com/morgannprice/fasttree/blob/main/index.html Example of a FASTA formatted sequence entry. Text after the first space on a description line is ignored by default. ```fasta >Ecoli arcA protein SEQUENCE ``` -------------------------------- ### CompareTree.pl Usage Example Source: https://github.com/morgannprice/fasttree/blob/main/treecmp.txt Compares two trees in Newick format and outputs a comparison table to standard output. It also reports similarity metrics to standard error. ```bash CompareTree.pl -tree tree1 -versus tree2 > comparison_table ``` -------------------------------- ### Phylip Interleaved Format Example Source: https://github.com/morgannprice/fasttree/blob/main/index.html Example of Phylip interleaved format. Sequence names can be of any length and must be separated by spaces from the sequence. ```phylip SeqName1 ATGC SeqName2 ATGC ``` -------------------------------- ### Phylip Interleaved Format with Blocks Source: https://github.com/morgannprice/fasttree/blob/main/index.html Example of Phylip interleaved format with multiple blocks. Sequence names must match the first block if repeated, or lines must start with spaces. ```phylip SeqName1 ATGC SeqName2 ATGC SeqName1 ATGC SeqName2 ATGC ``` -------------------------------- ### Compile FastTree on Mac/Unix Source: https://github.com/morgannprice/fasttree/blob/main/index.html Compile the C code for FastTree on Mac or Unix-like systems. Ensure you have gcc installed. The -march=native flag optimizes for your specific processor. ```bash gcc -O3 -fopenmp-simd -funsafe-math-optimizations -march=native -o FastTree FastTree.c -lm ``` -------------------------------- ### Running CompareToBootstrap.pl with MOTree.pm Source: https://github.com/morgannprice/fasttree/blob/main/treecmp.txt This command shows how to run the CompareToBootstrap.pl script, ensuring the MOTree.pm module is accessible by specifying its directory using the -I option. ```bash perl -I directory_containing_MOTree CompareToBootstrap.pl arguments... ``` -------------------------------- ### View FastTree Version and Options Source: https://github.com/morgannprice/fasttree/blob/main/index.html Run FastTree without arguments or with the -help option to display the current version and a list of available command-line options. ```bash FastTree ``` ```bash FastTree -help ``` -------------------------------- ### CompareToBootstrap Alternative Usage Source: https://github.com/morgannprice/fasttree/blob/main/treecmp.html An alternative command-line invocation for CompareToBootstrap.pl. ```bash CompareToBootstrap main_tree bootstrapped_trees > new_tree ``` -------------------------------- ### CompareToBootstrap.pl Usage Source: https://github.com/morgannprice/fasttree/blob/main/treecmp.html Compares a main phylogenetic tree against bootstrapped trees to generate a new tree with bootstrap values as internal node names. ```bash CompareToBootstrap.pl -tree main_tree -boot bootstrapped_trees > new_tree ``` -------------------------------- ### Perform Tree Comparison with CONSEL Source: https://github.com/morgannprice/fasttree/blob/main/index.html After converting log files to PAUP format, use CONSEL tools like makermt, consel, and catpv to perform statistical tests on tree topologies. ```bash makermt --paup top12.txt consel top12 catpv top12.pv ``` -------------------------------- ### Option for Logging Per-Site Likelihoods Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt When using the -gamma option, you can also enable the -log option to report per-site likelihoods. This provides more detailed information about the model's fit to the data. ```bash -gamma -log ``` -------------------------------- ### Compare Tree Likelihoods with Gamma Distribution Source: https://github.com/morgannprice/fasttree/blob/main/index.html Use the -gamma option to report the Gamma20 likelihood. This allows for comparable likelihoods across runs. The -intree option with -gamma -nome -mllen can be used to reoptimize branch lengths for a fixed topology. ```bash ./FastTree -gamma -nt -gtr -nome -mllen -intree topology1 -log topology1.log alignment.p > topology1.ftlen ./FastTree -gamma -nt -gtr -nome -mllen -intree topology2 -log topology2.log alignment.p > topology2.ftlen ``` -------------------------------- ### Option to Read Transition Matrix Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt Use the -trans option to provide a transition matrix and stationary distribution from a file. This feature is applicable only to amino acid alignments. ```bash -trans ``` -------------------------------- ### Option for Gamma20 Log Likelihoods Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt Implement fast Gamma20 log likelihoods using the -gamma option. This accounts for rate variation across sites with a discrete gamma distribution and provides more accurate branch lengths. ```bash -gamma ``` -------------------------------- ### Enable Gamma Likelihoods Source: https://github.com/morgannprice/fasttree/blob/main/index.html Use the -gamma option to rescale branch lengths and compute Gamma20-based likelihoods. This option may slightly increase runtime. ```bash FastTree -gamma < alignment_file > tree_file ``` -------------------------------- ### Infer Tree for Protein Alignment (JTT+CAT) Source: https://github.com/morgannprice/fasttree/blob/main/index.html Use this command to infer a phylogenetic tree for a protein alignment using the JTT+CAT model. Input can be piped or provided as a file. ```bash FastTree < alignment_file > tree_file ``` ```bash FastTree alignment.file > tree_file ``` -------------------------------- ### Option for Wag Model Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt Use the -wag option, contributed by Siavash Mirarab at UT Austin, for specific alignment modeling. ```bash -wag ``` -------------------------------- ### Convert FastTree Log to PAUP Format Source: https://github.com/morgannprice/fasttree/blob/main/index.html Use the GammaLogToPaup.pl script to reformat per-site likelihoods from FastTree log files for use with CONSEL. This enables Shimodaira-Hasegawa (SH) and approximately unbiased (AU) tests. ```bash perl GammaLogToPaup.pl topology1.log topology2.log > top12.txt ``` -------------------------------- ### Infer Tree for Protein Alignment (WAG+CAT or LG+CAT) Source: https://github.com/morgannprice/fasttree/blob/main/index.html Use the -wag or -lg options to specify the WAG+CAT or LG+CAT models for protein alignment tree inference. ```bash FastTree -wag < alignment_file > tree_file ``` ```bash FastTree -lg < alignment_file > tree_file ``` -------------------------------- ### Option for Output File Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt The -out option allows users to specify an output file for the results. This feature was added in response to popular demand. ```bash -out ``` -------------------------------- ### Compile Multi-threaded FastTreeMP on Mac/Unix Source: https://github.com/morgannprice/fasttree/blob/main/index.html Compile the multi-threaded version of FastTree (FastTreeMP) on Mac or Unix-like systems. This requires OpenMP support. The -DOPENMP flag enables multi-threading. ```bash gcc -DOPENMP -O3 -fopenmp -fopenmp-simd -funsafe-math-optimizations -march=native -o FastTree FastTree.c -lm ``` -------------------------------- ### Compile-time Option for Single-Precision Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt Compile with -DUSE_SINGLE if lower memory usage is required. This option switches FastTree to single-precision floating-point calculations. ```bash -DUSE_SINGLE ``` -------------------------------- ### Infer Tree for Nucleotide Alignment (GTR+CAT) Source: https://github.com/morgannprice/fasttree/blob/main/index.html Use this command to infer a phylogenetic tree for a nucleotide alignment with the GTR+CAT model. The -gtr and -nt flags are required. ```bash FastTree -gtr -nt < alignment.file > tree_file ``` ```bash FastTree -gtr -nt alignment_file > tree_file ``` -------------------------------- ### Option for Le/Gascuel Model Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt Add the -lg option to utilize the Le/Gascuel model for amino acid substitutions. This option was added thanks to contributions from researchers at Oakland University. ```bash -lg ``` -------------------------------- ### Infer Tree for Nucleotide Alignment (Jukes-Cantor + CAT) Source: https://github.com/morgannprice/fasttree/blob/main/index.html If -gtr is not specified, FastTree defaults to the Jukes-Cantor + CAT model for nucleotide alignments. ```bash FastTree -nt < alignment.file > tree_file ``` -------------------------------- ### Compile-time Option for Double-Precision Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt Compile with -DUSE_DOUBLE to enable double-precision floating-point calculations. This is recommended for more accurate shorter branch lengths, especially for wide alignments or very similar sequences. ```bash -DUSE_DOUBLE ``` -------------------------------- ### Read Multiple Alignments in Phylip Format Source: https://github.com/morgannprice/fasttree/blob/main/index.html Use the -n option to specify the number of alignments to expect when reading multiple alignments in a single Phylip formatted file. ```bash FastTree -n < num_alignments > alignment.file ``` -------------------------------- ### Compilation Flags for Auto-Vectorization Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt Use these flags to enable auto-vectorization (AVX2 instructions) for x86 machines during compilation. This can significantly improve performance for floating-point operations. ```bash gcc -fopen-simd -march=native ``` ```bash gcc -fopen-simd -march=core-avx2 ``` -------------------------------- ### Option for Quote Functionality Source: https://github.com/morgannprice/fasttree/blob/main/ChangeLog.txt The -quote option, contributed by Samuel Shepard at the CDC, provides specific functionality related to quoting. ```bash -quote ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.