Seedling

Quick and easy molecular phylogenies.

                            ╭ MT499915.1 Felis catus (Domestic cat)
                      ╭ 100 ┤
                      │     ╰ KP202275.1 Felis silvestris lybica (Near Eastern wildcat)
                ╭ 100 ┤
                │     ╰────── NC_028310.1 Felis silvestris (Wild cat)
          ╭ 100 ┤
          │     ╰──────────── KP202273.1 Felis silvestris bieti (Chinese desert cat)
     ╭ 99 ┤
     │    ╰────────────────── NC_028308.1 Felis margarita (Sand cat)
─ 97 ┤
     │    ╭────────────────── NC_028309.1 Felis nigripes (Black-footed cat)
     ╰ 97 ┤
          ╰────────────────── NC_028307.1 Felis chaus (Jungle cat)

Installation

Clone this repository to your local machine with git, then install with Python.

> git clone https://github.com/shanedrabing/seedling.git
> cd seedling
> python setup.py install

Hint: setup.py will try to compile the binaries for both Windows and *NIX machines. This step assumes you have g++ installed. If you run into issues, either install g++ or take a look at the compilation scripts in the src folder.

Getting Started

Run the program with Python.

> python seedling.py

Example Usage

This is what the console output looks like:

Please enter taxa searches on any line:

Felis
                  "Felis" search: 2.8 sec
Canis
                   "Felis" prune: 6.7 sec
                  "Canis" search: 5.3 sec
                   "Felis" score: 0.7 sec
                   "Felis" build: 0.1 sec
                    "Felis" done: 10.3 sec
                   "Canis" prune: 11.5 sec
                   "Canis" score: 3.5 sec
                   "Canis" build: 0.1 sec
                    "Canis" done: 20.4 sec
exit

Hint: wait for one process's "search" phase to end before you try another. I believe the network adapter doesn't like being hounded by multiple processes.

Example Output

The resultant "Felis" (cat genus) molecular phylogeny can be viewed above.

Here is our resultant "Canis" (dog genus) molecular phylogeny:

                                                                         ╭ MK948871.1 Canis lupus orion (Greenland wolf)
                                                                   ╭ 100 ┤
                                                                   │     ╰ MH746950.1 Canis lupus lupus (Eurasian wolf)
                                                             ╭ 100 ┤
                                                             │     ╰────── MZ042325.1 Canis lupus familiaris (Dog)
                                                       ╭ 100 ┤
                                                       │     ╰──────────── KC896375.1 Canis lupus campestris (Steppe wolf)
                                                 ╭ 100 ┤
                                                 │     ╰────────────────── KC461238.1 Canis lupus desertorum
                                           ╭ 100 ┤
                                           │     ╰──────────────────────── MZ042323.1 Canis lupus baileyi (Mexican gray wolf)
                                     ╭ 100 ┤
                                     │     ╰────────────────────────────── GQ374438.1 Canis lupus chanco (Mongolian wolf)
                               ╭ 100 ┤
                               │     │     ╭────────────────────────────── LC520095.1 Canis lupus hodophilax (Japanese wolf)
                               │     ╰ 100 ┤
                               │           ╰────────────────────────────── KF661092.1 Canis sp. Russia/33,500
                         ╭ 100 ┤
                         │     ╰────────────────────────────────────────── MH035676.1 Canis lupus dingo (Dingo)
                    ╭ 99 ┤
                    │    │    ╭─────────────────────────────────────────── NC_027956.1 Canis lupaster (African golden wolf)
                    │    ╰ 99 ┤
                    │         ╰─────────────────────────────────────────── KF573616.1 Canis lupus laniger (Tibetan wolf)
               ╭ 98 ┤
               │    │                      ╭────────────────────────────── MZ367921.1 Canis rufus (Red wolf)
               │    │                ╭ 100 ┤
               │    │                │     ╰────────────────────────────── MZ042357.1 Canis latrans (Coyote)
               │    │          ╭ 100 ┤
               │    │          │     ╰──────────────────────────────────── MZ367914.1 Canis lupus lycaon (Eastern Canadian wolf)
               │    │    ╭ 100 ┤
               │    │    │     ╰────────────────────────────────────────── MZ042364.1 Canis lupus (Gray wolf)
               │    ╰ 99 ┤
               │         ╰──────────────────────────────────────────────── KT448274.1 Canis aureus (Golden jackal)
          ╭ 97 ┤
          │    ╰────────────────────────────────────────────────────────── KT448280.1 Canis mesomelas (Black-backed jackal)
     ╭ 94 ┤
     │    ╰─────────────────────────────────────────────────────────────── KT448271.1 Canis adustus (Side-striped jackal)
─ 92 ┤
     ╰──────────────────────────────────────────────────────────────────── KF661079.1 Canis sp. Belgium/36,000

Hint: Check out the docs folder for more examples!

Warning

The method used for tree-construction is purely my effort, so it should be considered extremely inaccurate. Take the biological relevance of these trees with a grain of salt, but do have fun with the program!

It should be noted that this program only works on organisms with mitochondria, as it will search for complete mitochondrial DNA (mtDNA) genomes. Once it has done so, it trims the genome down to the mtDNA control region (CR). I use the mtDNA CR sequence from Canis latrans as the target for trimming, so the closer the evolutionary relationship between your search criteria and dogs, the more accurate the trimmed sequences will be.

To-Do

Some things I'm thinking about:

• Switch the method of trimming from Smith-Waterman to word methods for speed.
• Switch the method of scoring from Needleman-Wunsch (transition-transversion cost) to word methods as well.
• Scoring and building trees is currently pairwise, need to get that cost down.