mpboot

MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation

COMPILING INSTRUCTION SINCE 2020

• Clone the source code, unzip it, and rename to source
• Create folder build outside folder source
• Change directory to build
• Run cmake command:

cmake ../source -DIQTREE_FLAGS=sse4 -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++

• Replace sse4 by avx in above command if you decide to run MPBoot on AVX architecture
• Run make
• You will find the executable named mpboot once the make command is done.

PLACEMENT CORE

Parameter

• -pp_on: enable placement.
• -pp_n: number of available samples on tree.
• -pp_k: number of missing samples.
• -pp_tree: tree file.
• -pp_orig_spr: run spr without changing origin tree.
• -pp_test_spr: enable check correct tree.
• -pp_origin: origin tree file.
• -pp_zip_aln: alignment's zip file.
• -pp_zip_tree: tree's zip file.

Command

• Add missing samples to existing tree:
  ./mpboot -s <vcf file> -pp_tree <tree file> -pp_on -pp_n <existing samples> -pp_k <missing samples>
  Example:
  ./mpboot -s data/test5/1/added5.vcf -pp_tree data/test5/1/origin5.fasta.treefile -pp_on -pp_k 5 -pp_n 5
• Check if tree unchanged
  ./mpboot -s <vcf file> -pp_tree <tree file> -pp_origin <origin tree file> -pp_on -pp_test_spr -pp_k <missing samples> -pp_orig_spr
  Example:
  ./mpboot -s data/test5/1/added5.vcf -pp_tree addedTree.txt -pp_origin data/test5/1/origin5.fasta.treefile -pp_on -pp_test_spr -pp_k 5 -pp_orig_spr

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COMPILING INSTRUCTION PRIOR TO 2020

• Clone the source code, unzip it, and rename to source
• Change directory to source, run following commands to update the sub-repository

       git submodule init

       git submodule update

       cd pllrepo

       git checkout subufbootmp

• Create folder build outside folder source
• Change directory to build
• Run cmake command:

cmake ../source -DIQTREE_FLAGS=sse4 -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++

• Replace sse4 by avx in above command if you decide to run MPBoot on AVX architecture
• Run make
• You will find the executable named mpboot once the make command is done.