Main tool: UShER
Code repository: https://github.com/yatisht/usher
Basic information on how to use this tool:
- executable:
usher - help:
--help - version:
--version - description: UShER is a program for rapid, accurate placement of samples to existing phylogenies.
Full documentation: https://usher-wiki.readthedocs.io/en/latest/
Also contains (same version):
- matUtils
- matOptimize
- ripples
Additional tools installed via micromamba:
Name Version Build Channel
───────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
boost-cpp 1.85.0 h3c6214e_4 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
ca-certificates 2025.7.14 hbd8a1cb_0 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
icu 75.1 he02047a_0 conda-forge
isa-l 2.31.1 hb9d3cd8_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.44 h1423503_1 conda-forge
libasprintf 0.25.1 h8e693c7_0 conda-forge
libboost 1.85.0 h0ccab89_4 conda-forge
libboost-devel 1.85.0 h00ab1b0_4 conda-forge
libboost-headers 1.85.0 ha770c72_4 conda-forge
libcap 2.75 h39aace5_0 conda-forge
libcbor 0.10.2 hcb278e6_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libexpat 2.7.1 hecca717_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfido2 1.15.0 hdd1f21f_0 conda-forge
libgcc 15.1.0 h767d61c_3 conda-forge
libgcc-ng 15.1.0 h69a702a_3 conda-forge
libgettextpo 0.25.1 h5888daf_0 conda-forge
libgfortran 15.1.0 h69a702a_3 conda-forge
libgfortran-ng 15.1.0 h69a702a_3 conda-forge
libgfortran5 15.1.0 hcea5267_3 conda-forge
libgomp 15.1.0 h767d61c_3 conda-forge
libhwloc 2.12.1 default_h3d81e11_1000 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
liblzma-devel 5.8.1 hb9d3cd8_2 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenssl-static 3.5.1 hb9d3cd8_0 conda-forge
libpng 1.6.50 h943b412_0 conda-forge
libprotobuf 3.20.3 h3eb15da_0 conda-forge
libsqlite 3.50.3 hee844dc_1 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libudev1 257.7 hbe16f8c_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.13.8 h4bc477f_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
mpfr 4.2.1 h90cbb55_3 conda-forge
mpi 1.0 openmpi conda-forge
mysql-connector-c 6.1.11 h659d440_1008 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssh 10.0p1 hc830a30_0 conda-forge
openssl 3.5.1 h7b32b05_0 conda-forge
pip 25.1.1 pyh8b19718_0 conda-forge
protobuf 3.20.3 py311hcafe171_1 conda-forge
python 3.11.13 h9e4cc4f_0_cpython conda-forge
python_abi 3.11 8_cp311 conda-forge
readline 8.2 h8c095d6_2 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
tbb 2022.2.0 hb60516a_0 conda-forge
tbb-devel 2022.2.0 h74b38a2_0 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tzdata 2025b h78e105d_0 conda-forge
ucsc-fatovcf 482 hdc0a859_1 bioconda
usher 0.6.6 h719ac0c_1 bioconda
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xz 5.8.1 hbcc6ac9_2 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_2 conda-forge
xz-tools 5.8.1 hb9d3cd8_2 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
# create mutation annotated tree object
usher --tree global_phylo.nh --vcf global_samples.vcf --collapse-tree --save-mutation-annotated-tree global_phylo.pb
# place samples onto tree
usher --vcf new_samples.vcf --load-mutation-annotated-tree global_phylo.pb --write-uncondensed-final-tree