Main tool: pling
Code repository: https://github.com/iqbal-lab-org/pling
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda"
Name Version Build Channel
─────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aioeasywebdav 2.4.0 pyha770c72_0 conda-forge
aiohappyeyeballs 2.6.1 pyhd8ed1ab_0 conda-forge
aiohttp 3.12.13 py311h2dc5d0c_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
attrs 25.3.0 pyh71513ae_0 conda-forge
bcrypt 4.3.0 py311hdae7d1d_1 conda-forge
bitarray 3.4.2 py311h9ecbd09_0 conda-forge
bitstring 4.3.1 pyhd8ed1ab_0 conda-forge
boto3 1.38.46 pyhd8ed1ab_0 conda-forge
botocore 1.38.46 pyge310_1234567_0 conda-forge
brotli 1.1.0 hb9d3cd8_3 conda-forge
brotli-bin 1.1.0 hb9d3cd8_3 conda-forge
brotli-python 1.1.0 py311hfdbb021_3 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.6.15 hbd8a1cb_0 conda-forge
cachetools 5.5.2 pyhd8ed1ab_0 conda-forge
certifi 2025.6.15 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py311hf29c0ef_0 conda-forge
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
click 8.2.1 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 1.7.1 pyhe01879c_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
contourpy 1.3.2 py311hd18a35c_0 conda-forge
cryptography 45.0.4 py311hafd3f86_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
datrie 0.8.2 py311h9ecbd09_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 1.3.0 pyhd8ed1ab_0 conda-forge
filechunkio 1.8 py_2 conda-forge
fonttools 4.58.4 py311h2dc5d0c_0 conda-forge
freetype 2.13.3 ha770c72_1 conda-forge
frozenlist 1.6.0 py311h62d540b_0 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 2.25.1 pyhd8ed1ab_0 conda-forge
google-api-python-client 2.174.0 pyhff2d567_0 conda-forge
google-auth 2.40.3 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 3.1.1 pyhd8ed1ab_0 conda-forge
google-crc32c 1.7.1 py311h0973507_0 conda-forge
google-resumable-media 2.7.2 pyhd8ed1ab_2 conda-forge
googleapis-common-protos 1.70.0 pyhd8ed1ab_0 conda-forge
grpcio 1.71.0 py311h8825b61_1 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
httplib2 0.22.0 pyhd8ed1ab_1 conda-forge
humanfriendly 10.0 pyh707e725_8 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib-metadata 8.7.0 pyhe01879c_1 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 4.24.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2025.4.1 pyh29332c3_0 conda-forge
jupyter_core 5.8.1 pyh31011fe_0 conda-forge
kiwisolver 1.4.7 py311hd18a35c_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.43 h1423503_5 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libabseil 20250127.1 cxx17_hbbce691_0 conda-forge
libblas 3.9.0 32_h59b9bed_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_3 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_3 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_3 conda-forge
libcblas 3.9.0 32_he106b2a_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libdeflate 1.24 h86f0d12_0 conda-forge
libexpat 2.7.0 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfreetype 2.13.3 ha770c72_1 conda-forge
libfreetype6 2.13.3 h48d6fc4_1 conda-forge
libgcc 15.1.0 h767d61c_3 conda-forge
libgcc-ng 15.1.0 h69a702a_3 conda-forge
libgfortran 15.1.0 h69a702a_3 conda-forge
libgfortran5 15.1.0 hcea5267_3 conda-forge
libgomp 15.1.0 h767d61c_3 conda-forge
libgrpc 1.71.0 h8e591d7_1 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 32_h7ac8fdf_openblas conda-forge
liblapacke 3.9.0 32_he2f377e_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_0 conda-forge
libpng 1.6.49 h943b412_0 conda-forge
libprotobuf 5.29.3 h501fc15_1 conda-forge
libre2-11 2025.06.26 hba17884_0 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.50.2 h6cd9bfd_0 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libtiff 4.7.0 hf01ce69_5 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 py311h2dc5d0c_1 conda-forge
matplotlib-base 3.10.3 py311h2b939e6_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
multidict 6.6.3 py311h2dc5d0c_0 conda-forge
mummer 3.23 pl5321h503566f_21 bioconda
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.5 pyhe01879c_0 conda-forge
numpy 2.3.0 py311h519dc76_0 conda-forge
oauth2client 4.1.3 pyhd8ed1ab_1 conda-forge
openjpeg 2.5.3 h5fbd93e_0 conda-forge
openssl 3.5.0 h7b32b05_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.0 py311h7db5c69_0 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 11.2.1 py311h1322bbf_0 conda-forge
pip 25.1.1 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 4.3.8 pyhe01879c_0 conda-forge
pling 2.0.1 pyhdfd78af_0 bioconda
pluggy 1.6.0 pyhd8ed1ab_0 conda-forge
ply 3.11 pyhd8ed1ab_3 conda-forge
prettytable 3.16.0 pyhd8ed1ab_0 conda-forge
propcache 0.3.1 py311h2dc5d0c_0 conda-forge
proto-plus 1.26.1 pyhd8ed1ab_0 conda-forge
protobuf 5.29.3 py311h3a6f5f3_0 conda-forge
psutil 7.0.0 py311h9ecbd09_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pulp 2.7.0 py311h38be061_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 2.11.7 pyh3cfb1c2_0 conda-forge
pydantic-core 2.33.2 py311hdae7d1d_0 conda-forge
pygments 2.19.2 pyhd8ed1ab_0 conda-forge
pynacl 1.5.0 py311h9ecbd09_4 conda-forge
pyopenssl 25.1.0 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 8.4.1 pyhd8ed1ab_0 conda-forge
python 3.11.13 h9e4cc4f_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 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 3.11 7_cp311 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_1 conda-forge
pyyaml 6.0.2 py311h2dc5d0c_2 conda-forge
qhull 2020.2 h434a139_5 conda-forge
re2 2025.06.26 h9925aae_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
requests 2.32.4 pyhd8ed1ab_0 conda-forge
reretry 0.11.8 pyhd8ed1ab_1 conda-forge
rich 14.0.0 pyh29332c3_0 conda-forge
rpds-py 0.25.1 py311hdae7d1d_0 conda-forge
rsa 4.9.1 pyhd8ed1ab_0 conda-forge
s3transfer 0.13.0 pyhd8ed1ab_0 conda-forge
scipy 1.16.0 py311h2d3ef60_0 conda-forge
screed 1.1.3 pyhd8ed1ab_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
setuptools-scm 8.3.1 pyhd8ed1ab_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 4.9.3 hdfd78af_0 bioconda
sourmash-minimal 4.9.3 py311h3800737_0 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_hd72426e_102 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 0.16.0 pyh167b9f4_0 conda-forge
typer-slim 0.16.0 pyhe01879c_0 conda-forge
typer-slim-standard 0.16.0 hf964461_0 conda-forge
typing-extensions 4.14.0 h32cad80_0 conda-forge
typing-inspection 0.4.1 pyhd8ed1ab_0 conda-forge
typing_extensions 4.14.0 pyhe01879c_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
ubiquerg 0.8.0 pyhd8ed1ab_0 conda-forge
unicodedata2 16.0.0 py311h9ecbd09_0 conda-forge
uritemplate 4.2.0 pyhd8ed1ab_0 conda-forge
urllib3 2.5.0 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 py311h9ecbd09_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 1.20.1 py311h2dc5d0c_0 conda-forge
yte 1.8.1 pyha770c72_0 conda-forge
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zstandard 0.23.0 py311h9ecbd09_2 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