phykit 2.1.0__py3-none-any.whl

phykit/services/tree/treeness_over_rcv.py

@@ -0,0 +1,40 @@
+from enum import Enum
+from typing import Dict
+
+from .base import Tree
+from ..alignment.base import Alignment
+
+
+# TODO: Here next
+class FileFormat(Enum):
+    fasta = "fasta"
+    clustal = "clustal"
+    maf = "maf"
+    mauve = "mauve"
+    phylip = "phylip"
+    phylip_seq = "phylip-sequential"
+    phylip_rel = "phylip-relaxed"
+    stockholm = "stockholm"
+
+
+class TreenessOverRCV(Tree):
+    def __init__(self, args) -> None:
+        super().__init__(**self.process_args(args))
+
+    def run(self):
+        treeness = self.calculate_treeness()
+
+        aln = Alignment(alignment_file_path=self.alignment_file_path)
+        relative_composition_variability = aln.calculate_rcv()
+
+        treeness_over_rcv = treeness / relative_composition_variability
+
+        print(
+            f"{round(treeness_over_rcv, 4)}\t{round(treeness, 4)}\t{round(relative_composition_variability, 4)}"
+        )
+
+    def process_args(self, args) -> Dict[str, str]:
+        return dict(
+            tree_file_path=args.tree,
+            alignment_file_path=args.alignment,
+        )

phykit/version.py

@@ -0,0 +1 @@
+__version__ = "2.1.0"

phykit-2.1.0.dist-info/METADATA

@@ -0,0 +1,150 @@
+Metadata-Version: 2.4
+Name: phykit
+Version: 2.1.0
+Home-page: https://github.com/jlsteenwyk/phykit
+Author: Jacob L. Steenwyk
+Author-email: jlsteenwyk@gmail.com
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: biopython>=1.82
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: scipy>=1.11.3
+Requires-Dist: scikit-learn>=1.4.2
+Requires-Dist: cython
+Requires-Dist: tqdm>=4.65.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+
+<p align="center">
+  <a href="https://github.com/jlsteenwyk/phykit">
+    <img src="https://raw.githubusercontent.com/JLSteenwyk/PhyKIT/master/docs/_static/img/phykit_logo.png" alt="Logo" width="400">
+  </a>
+  <p align="center">
+    <a href="https://jlsteenwyk.com/PhyKIT/">Docs</a>
+    ·
+    <a href="https://github.com/jlsteenwyk/phykit/issues">Report Bug</a>
+    ·
+    <a href="https://github.com/jlsteenwyk/phykit/issues">Request Feature</a>
+  </p>
+    <p align="center">
+        <a href="https://github.com/JLSteenwyk/PhyKIT/actions" alt="Build">
+            <img src="https://img.shields.io/github/actions/workflow/status/JLSteenwyk/PhyKIT/ci.yml?branch=master">
+        </a>
+        <a href="https://codecov.io/gh/jlsteenwyk/phykit" alt="Coverage">
+          <img src="https://codecov.io/gh/jlsteenwyk/phykit/branch/master/graph/badge.svg?token=0J49I6441V">
+        </a>
+        <a href="https://github.com/jlsteenwyk/phykit/graphs/contributors" alt="Contributors">
+            <img src="https://img.shields.io/github/contributors/jlsteenwyk/phykit">
+        </a>
+        <a href="https://bsky.app/profile/jlsteenwyk.bsky.social" target="_blank" rel="noopener noreferrer">
+          <img src="https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff">
+        </a>
+        <br />
+        <a href="https://pepy.tech/badge/phykit">
+          <img src="https://static.pepy.tech/personalized-badge/phykit?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPi%20Downloads">
+        </a>
+        <a href="https://lbesson.mit-license.org/" alt="License">
+            <img src="https://img.shields.io/badge/License-MIT-blue.svg">
+        </a>
+        <a href="https://pypi.org/project/phykit/" alt="PyPI - Python Version">
+            <img src="https://img.shields.io/pypi/pyversions/phykit">
+        </a>
+        <a href="https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675?redirectedFrom=fulltext">
+          <img src="https://zenodo.org/badge/DOI/10.1093/bioinformatics/btab096.svg">
+        </a>
+    </p>
+</p>
+
+PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.<br /><br />
+If you found PhyKIT useful, please cite *PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data*. Bioinformatics. doi: [10.1093/bioinformatics/btab096](https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab096/6131675).
+<br /><br />
+
+---
+
+This documentation covers downloading and installing PhyKIT. Details about each function as well as tutorials for using PhyKIT are available in the <a href="https://jlsteenwyk.com/PhyKIT/">online documentation</a>.
+
+<br />
+
+**Quick Start**
+
+```shell
+# install
+pip install phykit
+# run
+phykit <function> <input file>
+```
+
+<br />
+
+**Installation** <br />
+
+**If you are having trouble installing PhyKIT, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**
+
+To install using *pip*, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:
+```shell
+# create virtual environment
+python -m venv .venv
+# activate virtual environment
+source .venv/bin/activate
+# install phykit
+pip install phykit
+```
+
+**Note, the virtual environment must be activated to use phykit.**
+
+After using PhyKIT, you may wish to deactivate your virtual environment and can do so using the following command:
+```shell
+# deactivate virtual environment
+deactivate
+```
+
+<br />
+
+Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:
+```shell
+# download
+git clone https://github.com/JLSteenwyk/PhyKIT.git
+cd PhyKIT/
+# create virtual environment
+python -m venv .venv
+# activate virtual environment
+source .venv/bin/activate
+# install
+make install
+```
+To deactivate your virtual environment, use the following command:
+```shell
+# deactivate virtual environment
+deactivate
+```
+**Note, the virtual environment must be activated to use phykit.**
+
+<br />
+
+To install via anaconda, execute the following command:
+```shell
+conda install bioconda::phykit
+```
+Visit here for more information:
+https://anaconda.org/bioconda/phykit
+
+<br />
+
+To test phykit installation, launch the help message
+
+```shell
+phykit -h
+```

phykit-2.1.0.dist-info/RECORD

@@ -0,0 +1,69 @@
+phykit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+phykit/__main__.py,sha256=bE_-UmloutmWmtdkWVZZ-kk_b6yLh1JloMPwSRd-CkY,113
+phykit/phykit.py,sha256=WQjA6dq8EjvXcrIryW0hD7EmUEgsAJf_pP7MzcJegdI,112299
+phykit/version.py,sha256=Xybt2skBZamGMNlLuOX1IG-h4uIxqUDGAO8MIGWrJac,22
+phykit/helpers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+phykit/helpers/boolean_argument_parsing.py,sha256=zD0h93gY-j_rAW9NRtRqcl9wWkvfjeBbEHV3yELO9Ck,282
+phykit/helpers/caching.py,sha256=7cRwj37Wg3pkxFbk7H3QztvqGFQgPp4q8cy4MuaDIxQ,5606
+phykit/helpers/files.py,sha256=H9s-BdfxCrvNBG_3PA13VyhkosgIX4BwoXyIzKpf8DQ,4164
+phykit/helpers/parallel.py,sha256=PP3I2NR1okxwBuk9ykz8CTlDcpLgOerX96gaiAGctFU,8668
+phykit/helpers/stats_summary.py,sha256=-6GYDMXGOE_GzTcYL0QRpg9_wSxUDNgKy-APeH_FGow,2266
+phykit/helpers/streaming.py,sha256=otvMXPCaewlAqP8Uz5ZtI4o2geGDB_GzYJOhVF6UHVk,4552
+phykit/services/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+phykit/services/base.py,sha256=5Uiy18sabf5RjuxujMhtrhrbxKZAqJLiNbbWcAIOV78,191
+phykit/services/alignment/__init__.py,sha256=6QtEQBp08WBlJKnYMbBETYYitSIJUrpJZPPKmEXh6ig,843
+phykit/services/alignment/alignment_length.py,sha256=KFMd05fEEQYDMvhTbpZ-Z3sjPB-5pxzGq3T9ig_YzPM,448
+phykit/services/alignment/alignment_length_no_gaps.py,sha256=oZE20pYLUBKNAybDI0AZnWF2pQ2lMRqFg31fE1wACO0,2012
+phykit/services/alignment/alignment_recoding.py,sha256=RltRrK5w7_f4aWd_9UKYuZ6LXu3aCpoFWuHInOcnZxw,2693
+phykit/services/alignment/base.py,sha256=bL2YcBD94hALnaeKAByZyfltY6771Pq2T2LjFLF_yG0,3543
+phykit/services/alignment/column_score.py,sha256=yNBPB25Cycsh3fepi-Sb8AOl8zN6tLvNUjxHewHEzZA,2155
+phykit/services/alignment/compositional_bias_per_site.py,sha256=ZeQpYqizf6x3CxcXfeRdUK6pGIDlDm7Q4vv1Bk-0aqQ,3296
+phykit/services/alignment/create_concatenation_matrix.py,sha256=0ZZH6vN8FlOFs42s6tn1pZCiWZfARnWJ4pHBKgOiA2g,10171
+phykit/services/alignment/dna_threader.py,sha256=LaP-Aor-vG1tacEKcf7OmSxtJuLLxlMePUtFpd3ehYk,5337
+phykit/services/alignment/evolutionary_rate_per_site.py,sha256=97bfdKh-5fZ0vog27nCmGQvqRHu-zZ2Q6VN4EaPp2I8,2723
+phykit/services/alignment/faidx.py,sha256=RDvv-_yqaq9zHwBShE7tcWi9VBOwAS1XK4yaqltEmg8,564
+phykit/services/alignment/gc_content.py,sha256=WYDeDywBhyfXJB-KRGujKml3HWo5thUln1tWaqIDaxs,3075
+phykit/services/alignment/pairwise_identity.py,sha256=Xckas7ezlySU_Fo0vWBzqI8a9cu5tru1SkGRJP9GbpU,5932
+phykit/services/alignment/parsimony_informative_sites.py,sha256=vsdlt9tpTXiqF8BI2Bv4IRRGab-wztt3Us4ntArHEus,2651
+phykit/services/alignment/rcv.py,sha256=Vsz8otx2WWYYFho4uE0hYCd6w93Xwx2uGKcXhGSJa6Y,435
+phykit/services/alignment/rcvt.py,sha256=2inrM0683cPdLGZXomCjehMlin_vWeR_B_r9-ASAjcs,1863
+phykit/services/alignment/rename_fasta_entries.py,sha256=qM2d4h7h9usagxBfTZwLHfUMbVI1RJU5kiYldTsngT8,1647
+phykit/services/alignment/sum_of_pairs_score.py,sha256=-VUctpI1YJrbjOAKaEiyRwInqmcB8_J5tqbdoUijP1g,6798
+phykit/services/alignment/variable_sites.py,sha256=QoB9QfV1sgJZc1Kq7D0SMR4h-VAO-M8XTuIz0ESF0_o,1672
+phykit/services/tree/__init__.py,sha256=5JXLKkqGN3Z6AgoQjLZhOTo_8H4yjsZlsDqCtlhH0vw,1372
+phykit/services/tree/base.py,sha256=PPx5neXZsGesXmjQMxwL6g_fz6UAgYIo2cMKkh2-yBs,5820
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+phykit/services/tree/branch_length_multiplier.py,sha256=jYjPFW6cJdMkCsIeKpf30kvEDz8IIgrnzm51QEBd1Ys,1126
+phykit/services/tree/collapse_branches.py,sha256=2ec5K9pJkwsEM8iZnQ9anJKe9INnUyNY3-kl0CQazuU,816
+phykit/services/tree/covarying_evolutionary_rates.py,sha256=qRHSBGtDKVeunu4TOgxP9O8lf8xMoLYKkBghe3SJ-K8,10625
+phykit/services/tree/dvmc.py,sha256=2tU-7JQ8CtojiIevylvrjl06tCJrOk029uJSyq7nXI0,1060
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+phykit/services/tree/internal_branch_stats.py,sha256=_hOqIENDTbyWwzta2q7dSlokG-ms5nDbuMFdywuWjKI,2294
+phykit/services/tree/internode_labeler.py,sha256=ieoU3crVwYn4QCfFjro9vTPd9VcwWJN5JfM2JZdl4JY,917
+phykit/services/tree/last_common_ancestor_subtree.py,sha256=xHYlIMmjLFPjnqoghXeRj0aHC_D-cyCNqt7srntdKXk,1088
+phykit/services/tree/lb_score.py,sha256=pofW3qmWX7AygjAu4IuUqozsMcuWrYVLgG1nnVcuYSE,6648
+phykit/services/tree/monophyly_check.py,sha256=TXHAUgoavZ9Nk7PDUcrTrYRxFKv7YJDJzFSLCMKzTEI,3545
+phykit/services/tree/nearest_neighbor_interchange.py,sha256=T-tNn7T7iSXMdFvnXheF06B63L5ftxDAM0ur42wM-lc,5653
+phykit/services/tree/patristic_distances.py,sha256=jEk5Qwq1Qu_ASA4pi2rEF9uWxhpYXz6QgRxnj5JrfRs,3776
+phykit/services/tree/polytomy_test.py,sha256=tx6akImmlhxNwFRjrPDtHbqevrqajNNsLXuhC9hxRT8,21065
+phykit/services/tree/print_tree.py,sha256=7yJNjrfXsh6CSvp6E5rEE9IbzpAsZc6bss_O2G5mEFU,716
+phykit/services/tree/prune_tree.py,sha256=47vu9-awiTRJNdzNfb1fS7FlgzJtjUMUnjXO_8qYrHw,1206
+phykit/services/tree/rename_tree_tips.py,sha256=9ToyYtJkJljwoVN1ni37uva5qeW9Hd0MB06slTQpKfk,1707
+phykit/services/tree/rf_distance.py,sha256=zn1indM8GGQNbQKyyiL3tk_T0MbZgJozJSRQ_970RhI,5237
+phykit/services/tree/root_tree.py,sha256=4fwe_yRg3pO15FAG1Jse2JSIqYckpOcXwCT_lw26p2k,962
+phykit/services/tree/saturation.py,sha256=A6AJ2TsWWcrcyve8rLMcVqjfeHo4fHuOB43PBbdJfCE,7034
+phykit/services/tree/spurious_sequence.py,sha256=lExV6ogxJCTbGWFusgY3uqBZYXMghq2xG2P6qYgvtYM,2122
+phykit/services/tree/terminal_branch_stats.py,sha256=BtRkvRNp-A53St6B3qEowrN4oq-nhAIizR2g55pBImo,2575
+phykit/services/tree/tip_labels.py,sha256=JDhNo-I3jcG1nAEKWSfWJXEH4Imub4iIc2dTbHW5Las,462
+phykit/services/tree/tip_to_tip_distance.py,sha256=OHP0Wag6aIYnO_20oTtfWiDxqaeZRTNQi-pZJo2bvMA,1081
+phykit/services/tree/tip_to_tip_node_distance.py,sha256=3hUncROX9-oTbVnt-WNlaVJDQnIXNK5magN5pbD0AWc,1085
+phykit/services/tree/total_tree_length.py,sha256=vdOT7qygyFHavlB0dwfScFcLL3S6b4NikAGipjE_OKs,664
+phykit/services/tree/treeness.py,sha256=xDisu6Co0hfeWo3fPG3SFXKgL6tt2vS9rgk8tNFqMWc,409
+phykit/services/tree/treeness_over_rcv.py,sha256=JXf-LzDvV5ckj6DvaDrKOjyCiVN-UdLcMaQqUA6BBDI,1056
+phykit-2.1.0.dist-info/licenses/LICENSE.md,sha256=S5sMP_xz_OTEdzTX7xK9cLnSzcSjv3asDzo17b4sPZ4,1078
+phykit-2.1.0.dist-info/METADATA,sha256=hK7JsTrjI0c9J86MakxBOENb66E8YVp0-_1VX627Xow,5334
+phykit-2.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+phykit-2.1.0.dist-info/entry_points.txt,sha256=Sjk6OdXt2ROk3mbU5z7_k5ps3akjoN20CclzRACtGVw,5814
+phykit-2.1.0.dist-info/top_level.txt,sha256=bOMmJQrzcB3UDlMLE7OeP__Ek0x3D6KlKUI4XhDw-0U,7
+phykit-2.1.0.dist-info/RECORD,,

phykit-2.1.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

phykit-2.1.0.dist-info/entry_points.txt

@@ -0,0 +1,121 @@
+[console_scripts]
+phykit = phykit.phykit:main
+pk_al = phykit.phykit:alignment_length
+pk_alignment_length = phykit.phykit:alignment_length
+pk_alignment_length_no_gaps = phykit.phykit:alignment_length_no_gaps
+pk_alignment_recoding = phykit.phykit:alignment_recoding
+pk_aln_len = phykit.phykit:alignment_length
+pk_aln_len_no_gaps = phykit.phykit:alignment_length_no_gaps
+pk_aln_recoding = phykit.phykit:alignment_recoding
+pk_alng = phykit.phykit:alignment_length_no_gaps
+pk_bipartition_support_stats = phykit.phykit:bipartition_support_stats
+pk_blm = phykit.phykit:branch_length_multiplier
+pk_branch_length_multiplier = phykit.phykit:branch_length_multiplier
+pk_bss = phykit.phykit:bipartition_support_stats
+pk_cb = phykit.phykit:collapse_branches
+pk_cbps = phykit.phykit:compositional_bias_per_site
+pk_cc = phykit.phykit:create_concatenation_matrix
+pk_clan_check = phykit.phykit:hidden_paralogy_check
+pk_collapse = phykit.phykit:collapse_branches
+pk_collapse_branches = phykit.phykit:collapse_branches
+pk_column_score = phykit.phykit:column_score
+pk_comp_bias_per_site = phykit.phykit:compositional_bias_per_site
+pk_compositional_bias_per_site = phykit.phykit:compositional_bias_per_site
+pk_covarying_evolutionary_rates = phykit.phykit:covarying_evolutionary_rates
+pk_cover = phykit.phykit:covarying_evolutionary_rates
+pk_create_concat = phykit.phykit:create_concatenation_matrix
+pk_create_concatenation_matrix = phykit.phykit:create_concatenation_matrix
+pk_cs = phykit.phykit:column_score
+pk_degree_of_violation_of_a_molecular_clock = phykit.phykit:dvmc
+pk_dvmc = phykit.phykit:dvmc
+pk_erps = phykit.phykit:evolutionary_rate_per_site
+pk_evo_rate = phykit.phykit:evolutionary_rate
+pk_evo_rate_per_site = phykit.phykit:evolutionary_rate_per_site
+pk_evolutionary_rate = phykit.phykit:evolutionary_rate
+pk_evolutionary_rate_per_site = phykit.phykit:evolutionary_rate_per_site
+pk_faidx = phykit.phykit:faidx
+pk_gc = phykit.phykit:gc_content
+pk_gc_content = phykit.phykit:gc_content
+pk_ge = phykit.phykit:faidx
+pk_get_entry = phykit.phykit:faidx
+pk_hidden_paralogy_check = phykit.phykit:hidden_paralogy_check
+pk_ibs = phykit.phykit:internal_branch_stats
+pk_il = phykit.phykit:internode_labeler
+pk_internal_branch_stats = phykit.phykit:internal_branch_stats
+pk_internode_labeler = phykit.phykit:internode_labeler
+pk_is_monophyletic = phykit.phykit:monophyly_check
+pk_labels = phykit.phykit:tip_labels
+pk_last_common_ancestor_subtree = phykit.phykit:last_common_ancestor_subtree
+pk_lb_score = phykit.phykit:lb_score
+pk_lbs = phykit.phykit:lb_score
+pk_lca_subtree = phykit.phykit:last_common_ancestor_subtree
+pk_long_branch_score = phykit.phykit:lb_score
+pk_monophyly_check = phykit.phykit:monophyly_check
+pk_nearest_neighbor_interchange = phykit.phykit:nearest_neighbor_interchange
+pk_nni = phykit.phykit:nearest_neighbor_interchange
+pk_p2n = phykit.phykit:thread_dna
+pk_pairwise_id = phykit.phykit:pairwise_identity
+pk_pairwise_identity = phykit.phykit:pairwise_identity
+pk_pal2nal = phykit.phykit:thread_dna
+pk_parsimony_informative_sites = phykit.phykit:parsimony_informative_sites
+pk_patristic_distances = phykit.phykit:patristic_distances
+pk_pd = phykit.phykit:patristic_distances
+pk_pi = phykit.phykit:pairwise_identity
+pk_pis = phykit.phykit:parsimony_informative_sites
+pk_polyt = phykit.phykit:polytomy_test
+pk_polyt_test = phykit.phykit:polytomy_test
+pk_polytomy_test = phykit.phykit:polytomy_test
+pk_print = phykit.phykit:print_tree
+pk_print_tree = phykit.phykit:print_tree
+pk_prune = phykit.phykit:prune_tree
+pk_prune_tree = phykit.phykit:prune_tree
+pk_pt = phykit.phykit:print_tree
+pk_ptt = phykit.phykit:polytomy_test
+pk_rcv = phykit.phykit:rcv
+pk_rcvt = phykit.phykit:rcvt
+pk_recode = phykit.phykit:alignment_recoding
+pk_rel_comp_var = phykit.phykit:rcv
+pk_rel_comp_var_taxon = phykit.phykit:rcvt
+pk_relative_composition_variability = phykit.phykit:rcv
+pk_relative_composition_variability_taxon = phykit.phykit:rcvt
+pk_rename_fasta = phykit.phykit:rename_fasta_entries
+pk_rename_fasta_entries = phykit.phykit:rename_fasta_entries
+pk_rename_tips = phykit.phykit:rename_tree_tips
+pk_rename_tree = phykit.phykit:rename_tree_tips
+pk_rename_tree_tips = phykit.phykit:rename_tree_tips
+pk_rf = phykit.phykit:rf_distance
+pk_rf_dist = phykit.phykit:rf_distance
+pk_rf_distance = phykit.phykit:rf_distance
+pk_robinson_foulds_distance = phykit.phykit:rf_distance
+pk_root = phykit.phykit:root_tree
+pk_root_tree = phykit.phykit:root_tree
+pk_rt = phykit.phykit:root_tree
+pk_sat = phykit.phykit:saturation
+pk_saturation = phykit.phykit:saturation
+pk_sop = phykit.phykit:sum_of_pairs_score
+pk_sops = phykit.phykit:sum_of_pairs_score
+pk_spurious_seq = phykit.phykit:spurious_sequence
+pk_spurious_sequence = phykit.phykit:spurious_sequence
+pk_ss = phykit.phykit:spurious_sequence
+pk_sum_of_pairs_score = phykit.phykit:sum_of_pairs_score
+pk_t2t = phykit.phykit:tip_to_tip_distance
+pk_t2t_dist = phykit.phykit:tip_to_tip_distance
+pk_t2t_nd = phykit.phykit:tip_to_tip_node_distance
+pk_t2t_node_dist = phykit.phykit:tip_to_tip_node_distance
+pk_tbs = phykit.phykit:terminal_branch_stats
+pk_terminal_branch_stats = phykit.phykit:terminal_branch_stats
+pk_thread_dna = phykit.phykit:thread_dna
+pk_tip_labels = phykit.phykit:tip_labels
+pk_tip_to_tip_distance = phykit.phykit:tip_to_tip_distance
+pk_tip_to_tip_node_distance = phykit.phykit:tip_to_tip_node_distance
+pk_tl = phykit.phykit:tip_labels
+pk_tness = phykit.phykit:treeness
+pk_tor = phykit.phykit:treeness_over_rcv
+pk_total_tree_length = phykit.phykit:total_tree_length
+pk_toverr = phykit.phykit:treeness_over_rcv
+pk_tree_labels = phykit.phykit:tip_labels
+pk_tree_len = phykit.phykit:total_tree_length
+pk_treeness = phykit.phykit:treeness
+pk_treeness_over_rcv = phykit.phykit:treeness_over_rcv
+pk_variable_sites = phykit.phykit:variable_sites
+pk_vs = phykit.phykit:variable_sites

phykit-2.1.0.dist-info/licenses/LICENSE.md

@@ -0,0 +1,7 @@
+Copyright (c) 2020 Jacob L. Steenwyk and contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

phykit-2.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+phykit