Main tool: pling
Code repository: https://github.com/iqbal-lab-org/pling
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
aioeasywebdav 2.4.0 py39hf3d152e_1001 conda-forge
aiohappyeyeballs 2.6.1 pyhd8ed1ab_0 conda-forge
aiohttp 3.11.16 py39h9399b63_0 conda-forge
aiosignal 1.3.2 pyhd8ed1ab_0 conda-forge
amply 0.1.6 pyhd8ed1ab_1 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
appdirs 1.4.4 pyhd8ed1ab_1 conda-forge
async-timeout 5.0.1 pyhd8ed1ab_1 conda-forge
attrs 25.3.0 pyh71513ae_0 conda-forge
bcrypt 4.3.0 py39he612d8f_0 conda-forge
bitstring 3.1.9 pyhd8ed1ab_0 conda-forge
boto3 1.37.31 pyhd8ed1ab_0 conda-forge
botocore 1.37.31 pyge38_1234567_0 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py39hf88036b_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.1.31 hbcca054_0 conda-forge
cachetools 4.2.4 pyhd8ed1ab_0 conda-forge
certifi 2025.1.31 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py39h15c3d72_0 conda-forge
charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge
click 8.1.8 pyh707e725_0 conda-forge
coin-or-cbc 2.10.12 h00e76a6_2 conda-forge
coin-or-cgl 0.60.9 h82e2f02_4 conda-forge
coin-or-clp 1.17.10 h8a7a1e7_1 conda-forge
coin-or-osi 0.108.11 h96cc833_4 conda-forge
coin-or-utils 2.11.12 h3a12e53_2 conda-forge
coincbc 2.10.12 2_metapackage conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
coloredlogs 15.0.1 pyhd8ed1ab_4 conda-forge
configargparse 1.7 pyhd8ed1ab_1 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
contourpy 1.3.0 py39h74842e3_2 conda-forge
cryptography 44.0.2 py39h7170ec2_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
datrie 0.8.2 py39h8cd3c5a_8 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecation 2.1.0 pyh9f0ad1d_0 conda-forge
dingii 0.0.1 pyhdfd78af_0 bioconda
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
dpath 2.2.0 pyha770c72_0 conda-forge
dropbox 12.0.2 pyhd8ed1ab_1 conda-forge
eido 0.2.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_1 conda-forge
filechunkio 1.8 py_2 conda-forge
fonttools 4.57.0 py39h9399b63_0 conda-forge
freetype 2.13.3 h48d6fc4_0 conda-forge
frozenlist 1.5.0 py39h9399b63_1 conda-forge
ftputil 5.1.0 pyhd8ed1ab_0 conda-forge
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.44 pyhff2d567_0 conda-forge
glpk 5.0 h445213a_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
google-api-core 2.24.2 pyhd8ed1ab_0 conda-forge
google-api-python-client 2.165.0 pyhff2d567_0 conda-forge
google-auth 2.38.0 pyhd8ed1ab_0 conda-forge
google-auth-httplib2 0.2.0 pyhd8ed1ab_1 conda-forge
google-cloud-core 2.4.3 pyhd8ed1ab_0 conda-forge
google-cloud-storage 3.1.0 pyhd8ed1ab_0 conda-forge
google-crc32c 1.7.1 py39h2cad9fb_0 conda-forge
google-resumable-media 2.7.2 pyhd8ed1ab_2 conda-forge
googleapis-common-protos 1.69.2 pyhd8ed1ab_0 conda-forge
grpcio 1.71.0 py39h169e510_0 conda-forge
httplib2 0.22.0 pyhd8ed1ab_1 conda-forge
humanfriendly 10.0 pyh707e725_8 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib-metadata 8.6.1 pyha770c72_0 conda-forge
importlib-resources 6.5.2 pyhd8ed1ab_0 conda-forge
importlib_metadata 8.6.1 hd8ed1ab_0 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_1 conda-forge
intervaltree 3.1.0 pyhd8ed1ab_1 conda-forge
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
jmespath 1.0.1 pyhd8ed1ab_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_1 conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_1 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
kiwisolver 1.4.7 py39h74842e3_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20250127.1 cxx17_hbbce691_0 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libdeflate 1.23 h4ddbbb0_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgfortran 14.2.0 h69a702a_2 conda-forge
libgfortran-ng 14.2.0 h69a702a_2 conda-forge
libgfortran5 14.2.0 hf1ad2bd_2 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
libgrpc 1.71.0 he753a82_0 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 31_h7ac8fdf_openblas conda-forge
liblapacke 3.9.0 31_he2f377e_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.29 pthreads_h94d23a6_0 conda-forge
libpng 1.6.47 h943b412_0 conda-forge
libprotobuf 5.29.3 h501fc15_0 conda-forge
libre2-11 2024.07.02 hba17884_3 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.49.1 hee588c1_2 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libtiff 4.7.0 hd9ff511_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.5.0 h851e524_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
logmuse 0.2.8 pyhd8ed1ab_1 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_1 conda-forge
markupsafe 3.0.2 py39h9399b63_1 conda-forge
matplotlib-base 3.9.4 py39h16632d1_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
multidict 6.3.2 py39h9399b63_0 conda-forge
mummer 3.23 pl5321h503566f_21 bioconda
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
numpy 2.0.2 py39h9cb892a_1 conda-forge
oauth2client 4.1.3 pyhd8ed1ab_1 conda-forge
openjpeg 2.5.3 h5fbd93e_0 conda-forge
openssl 3.5.0 h7b32b05_0 conda-forge
packaging 24.2 pyhd8ed1ab_2 conda-forge
pandas 2.2.3 py39h3b40f6f_2 conda-forge
paramiko 3.5.1 pyhd8ed1ab_0 conda-forge
pephubclient 0.4.4 pyhd8ed1ab_1 conda-forge
peppy 0.40.7 pyhd8ed1ab_2 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pillow 11.1.0 py39h15c0740_0 conda-forge
pip 25.0.1 pyh8b19718_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_2 conda-forge
plac 1.4.5 pyhd8ed1ab_0 conda-forge
plasnet 0.6.0 pyhdfd78af_1 bioconda
platformdirs 4.3.7 pyh29332c3_0 conda-forge
pling 2.0.0 pyhdfd78af_0 bioconda
pluggy 1.5.0 pyhd8ed1ab_1 conda-forge
ply 3.11 pyhd8ed1ab_3 conda-forge
prettytable 3.16.0 pyhd8ed1ab_0 conda-forge
propcache 0.2.1 py39h9399b63_1 conda-forge
proto-plus 1.26.1 pyhd8ed1ab_0 conda-forge
protobuf 5.29.3 py39hbeaf701_0 conda-forge
psutil 7.0.0 py39h8cd3c5a_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pulp 2.7.0 py39hf3d152e_1 conda-forge
pyasn1 0.6.1 pyhd8ed1ab_2 conda-forge
pyasn1-modules 0.4.2 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pydantic 2.11.3 pyh3cfb1c2_0 conda-forge
pydantic-core 2.33.1 py39h3506688_0 conda-forge
pygments 2.19.1 pyhd8ed1ab_0 conda-forge
pynacl 1.5.0 py39h8cd3c5a_4 conda-forge
pyopenssl 25.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pysftp 0.2.9 py_1 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytest 8.3.5 pyhd8ed1ab_0 conda-forge
python 3.9.21 h85ef794_2_cpython conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge
python-irodsclient 2.1.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 6_cp39 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_1 conda-forge
pyyaml 6.0.2 py39h9399b63_2 conda-forge
qhull 2020.2 h434a139_5 conda-forge
re2 2024.07.02 h9925aae_3 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
reretry 0.11.8 pyhd8ed1ab_1 conda-forge
rich 14.0.0 pyh29332c3_0 conda-forge
rpds-py 0.24.0 py39h3506688_0 conda-forge
rsa 4.9 pyhd8ed1ab_1 conda-forge
s3transfer 0.11.4 pyhd8ed1ab_0 conda-forge
scipy 1.13.1 py39haf93ffa_0 conda-forge
screed 1.1.3 pyhd8ed1ab_0 conda-forge
setuptools 78.1.0 pyhff2d567_0 conda-forge
shellingham 1.5.4 pyhd8ed1ab_1 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
slacker 0.14.0 pyhd8ed1ab_1 conda-forge
smart_open 7.1.0 pyhd8ed1ab_0 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snakemake 7.32.4 hdfd78af_1 bioconda
snakemake-minimal 7.32.4 pyhdfd78af_1 bioconda
sortedcontainers 2.4.0 pyhd8ed1ab_1 conda-forge
sourmash 4.8.4 hdfd78af_0 bioconda
sourmash-minimal 4.8.4 py39h9fdd4d6_1 conda-forge
stone 3.3.2 pyhd8ed1ab_0 conda-forge
stopit 1.1.2 pyhd8ed1ab_1 conda-forge
tabulate 0.9.0 pyhd8ed1ab_2 conda-forge
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
toposort 1.10 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
typer 0.15.2 pyhff008b6_0 conda-forge
typer-slim 0.15.2 pyh29332c3_0 conda-forge
typer-slim-standard 0.15.2 h801b22e_0 conda-forge
typing-extensions 4.13.1 hf5ce1d7_0 conda-forge
typing-inspection 0.4.0 pyhd8ed1ab_0 conda-forge
typing_extensions 4.13.1 pyh29332c3_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
ubiquerg 0.8.0 pyhd8ed1ab_0 conda-forge
unicodedata2 16.0.0 py39h8cd3c5a_0 conda-forge
uritemplate 4.1.1 pyhd8ed1ab_1 conda-forge
urllib3 1.26.19 pyhd8ed1ab_0 conda-forge
veracitools 0.1.3 py_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wrapt 1.17.2 py39h8cd3c5a_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.18.3 py39h9399b63_1 conda-forge
yte 1.7.0 pyha770c72_1 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Basic information on how to use this tool:
- executable:
pling - help:
-h,--help - version:
--version - description:
Pling is a software workflow for plasmid analysis using rearrangement distances, specifically the Double Cut and Join Indel (DCJ-Indel) distance. By intelligently combining containment distance (shared content as fraction of the smaller) and DCJ-indel distance (“how far apart evolutionarily” in a structural sense), and by preventing shared mobile elements from clouding the issue, it infers clusters of related plasmids.
Additional information:
Frolova, D., Lima, L., Roberts, L. W., Bohnenkämper, L., Wittler, R., Stoye, J., & Iqbal, Z. (2024). Applying rearrangement distances to enable plasmid epidemiology with pling. Microbial Genomics, 10(10). https://doi.org/10.1099/mgen.0.001300
Full documentation: https://pling.readthedocs.io/latest/
# input is a text file of a list of paths to fasta files
pling input.txt output_dir align