voseq

:evergreen_tree: VoSeq is a database to store voucher and sequence data

https://github.com/voseq/voseq

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:evergreen_tree: VoSeq is a database to store voucher and sequence data

README.rst

=====
VoSeq
=====

|BuildStatus| |CoverageStatus| |Python_versions| |Chat|

.. |BuildStatus| image:: https://travis-ci.org/VoSeq/VoSeq.svg
    :target: https://travis-ci.org/VoSeq/VoSeq

.. |CoverageStatus| image:: https://img.shields.io/coveralls/VoSeq/VoSeq.svg
    :target: https://coveralls.io/r/VoSeq/VoSeq?branch=master

.. |Chat| image:: https://badges.gitter.im/Join%20Chat.svg
    :alt: Join the chat at https://gitter.im/VoSeq/VoSeq
    :target: https://gitter.im/VoSeq/VoSeq?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge

.. |Python_versions| image:: https://img.shields.io/badge/python-3.6%203.7-blue.svg
    :alt: Python versions


Contents
========

* `The new VoSeq is here`_
* `New features`_
* `Quick install of VoSeq using Docker (Recommended)`_
* `Installation instructions`_
* `Test database for development`_
* `Start a test server`_
* `Migrate VoSeq database`_
* `Set-up a publicly available web server`_
* `Administrate the server`_
* `Deployment of VoSeq`_
* `Upgrade VoSeq's software`_
* `Database backups`_

`Full documentation `__.

The new VoSeq is here
=====================

We have rebuilt VoSeq from scratch. We decided to migrate from PHP to
Python by using the framework Django. We also moved from MySQL to
PostgreSQL.

You can still download the old VoSeq v1.7.4 from
`here `__. But
be aware that we will not be doing maintenance of that code.

More details about the migration can be found in our `discussion
list `__.


New Features
============
Query suggestions for simple taxon searches:

.. image:: https://raw.githubusercontent.com/VoSeq/VoSeq/master/imgs/simple_search_suggestion.png

Quick install of VoSeq using Docker (Recommended)
=================================================
Docker allows setting up virtual machines that automatically installs all
dependencies and sets up configuration from a *recipe* contained in the Docker
file.

You need `Docker `__ installed in your
computer or server.

Assuming that you have installed [GIT](https://git-scm.com/downloads), you need
to get a copy of VoSeq into your hard-disk. From a console or terminal type the
following command:

.. code:: shell

	git clone https://github.com/VoSeq/VoSeq.git

Just go to the VoSeq's directory:

.. code:: shell

	cd VoSeq

And execute the following command:

.. code:: shell

    ./run/scripts/docker_upgrade

Once the process has finished, you will have a new Ubuntu virtual machine with
VoSeq installed. To enter this virtual machine:

.. code:: shell

    ./run/scripts/docker_compose exec app bash

To exit the virtual machine:

.. code:: shell

    exit

Import a test database into your Voseq installation: (1) enter the virtual
machine, (2) execute the command to import the database:

.. code:: shell

    ./run/scripts/docker_compose exec app bash
    python manage.py import_test_db

Set up an administrator account by using the command ``make admin``
(see `Administrate the server`_).

In your host system, open your brower and load this URL:
localhost:8081 to see your fresh installation of VoSeq.


Installation instructions
=========================

These instructions assume that your libraries are up to date and that you have Python, pip and
virtual environments installed. Python3 is recommended.

**Step 1: get VoSeq.**
Clone or `download `__ VoSeq to your preferred directory.
We recommend cloning VoSeq as it will be easier to do software upgrades with on single command:

* To clone VoSeq:

.. code:: shell

    git clone https://github.com/VoSeq/VoSeq.git


* To upgrade VoSeq to newer versions:

.. code:: shell

    cd /path/to/VoSeq
    git pull origin master

**Step 2: create a virtual environment and install dependencies.**
To ensure that all the dependencies will work without conflict, it is best to install them within a virtual environment.

.. code:: shell

    mkvirtualenv -p /usr/bin/python3 voseq_environment
    cd /path/to/VoSeq
    workon voseq_environment
    pip install -r requirements/testing.txt

Exit the virtual environment for now to continue from the shell:

.. code:: shell

    deactivate

**Step 3: download and install elasticsearch.**
Elasticsearch is needed to enable the advanced search tool and auto suggestions. By default, the
elasticsearch is enabled. You can disable it in the `config.json` file by using the key:value
`"ELASTICSEARCH": "false"`. In such case, only the general search will work.

Use elasticsearch versions 1.7.3 or below. The newer versions 2.0+ currently
do not work with VoSeq.
For elasticsearch, java needs to be installed. Mac users can download and install ``elasticsearch`` from here:
http://www.elasticsearch.org/overview/elkdownloads/. In Linux, you can do:

.. code:: shell

    wget https://download.elastic.co/elasticsearch/elasticsearch/elasticsearch-1.5.2.deb
    sudo dpkg -i elasticsearch-1.5.2.deb

The bin directory of elasticsearch should be added automatically to your PATH. If not, add the following
line to your ``.profile`` (Linux) or ``.bash_profile`` (macOSX) file:

.. code:: shell

    export PATH="$PATH:/path/to/elasticsearch/bin/"

**Step 4: download, install and configure PostgreSQL.**
For macOSX users we recommend to do it by downloading the Postgres.app from http://postgresapp.com.
Linux users can use apt-get:

.. code:: shell

    sudo apt-get install postgresql postgresql-contrib postgresql-server-dev-9.3

Create new role by typing:

.. code:: shell

    createuser --interactive

Enter the psql shell, create a password for this user and create a database for VoSeq:

.. code:: shell

    psql
    postgres=# ALTER ROLE postgres WITH PASSWORD 'hu8jmn3';
    postgres=# create database voseq;


In macOSX if you are using the Postgres.app, it my be enough to run:

.. code:: shell

    psql
    user.name=# CREATE DATABASE voseq;

To exit the psql shell:

.. code:: shell

    \q
    
Next, create a ``config.json`` file to keep the database variables:

.. code:: shell

    cd /path/to/Voseq
    touch config.json

and write in the following content:

.. code:: javascript

    {
    "SECRET_KEY": "create_a_secret_key",
    "DB_USER": "postgres",
    "DB_PASS": "hu8jmn3",
    "DB_NAME": "voseq",
    "DB_PORT": "5432",
    "DB_HOST": "localhost",
    "GOOGLE_MAPS_API_KEY": "get_a_google_map_api_key",
    "PHOTOS_REPOSITORY": "local",
    "ELASTICSEARCH": "false"
    }

If you want to host your photos in Flickr you need to change the last parameter
of your ``config.json`` file to ``"PHOTOS_REPOSITORY": "flickr"``.

If you followed the above instructions to the letter, the DB_USER will be "postgres" and the DB_PASS
will be "hu8jmn3". It is of recommended to come up with your own password.
Instructions to obtain a personal google map browser API key can be found
`here `__.
You need to create a **Google Maps JavaScript API** for yourself.

After following these four steps everything should be installed and ready to run. You can now choose
to either continue with adding real data migrated from VoSeq 1.x and setting up a publicly available
web server, or to first add some test data and test the set-up with a lightweight local server
included in the VoSeq package.

Test database for development
=============================

You can use test data to populate your PostgreSQL database, useful for
development.

First, enter the virtual environment:

.. code:: shell

    workon voseq_environment

Then, create tables for the database:

.. code:: shell

    cd /path/to/Voseq/
    make migrations

And import test data for your database:

.. code:: shell

    make test_import

Start a test server
===================

In Linux start elasticsearch as a service, then enter the virtual environment and then start the server:

.. code:: shell

    sudo service elasticsearch start
    workon voseq_environment
    cd /path/to/Voseq
    make serve

In macOSX if you do not have the ``service`` command, run
``elasticsearch`` in the background and then start the server (\*):

.. code:: shell

    elasticsearch -d
    cd /path/to/Voseq
    make serve

\* *Note that if you did not check to Start Postgres automatically after
login, you first have to go to Applications and start it manually from
there by clicking on the Postgres.app. Do this before running the
server.*

You now have a local webserver running. You can access it by opening this URL in your web browser:
``http://127.0.0.1:8000/`` and try all the buttons to see if they all work! Also notice the debug bar
on the right of the screen where you can check if all the configurations are correct.

Migrate VoSeq database
======================

If you have an existing Voseq 1.x database and want to migrate, you need to dump your MySQL database
into a XML file:

.. code:: shell

    cd /path/to/Voseq/
    mysqldump --xml voseq_database > dump.xml

Then use our script to migrate all your VoSeq data into a PostGreSQL
database.

.. code:: shell

    make migrations
    python voseq/manage.py migrate_db --dumpfile=dump.xml --settings=voseq.settings.local

If you have used a prefix for your tables in the old VoSeq, you can optionally input this as an
argument for the import script:

.. code:: shell

    python voseq/manage.py migrate_db --dumpfile=dump.xml --prefix=voseq_ --settings=voseq.settings.local


It might issue a warning message:

::

    WARNING:: Could not parse dateCreation properly.
    WARNING:: Using empty as date for `time_edited` for code Your_Vocher_Code

It means that the creation time for your voucher was probably empty or
similar to ``0000-00-00``. In that case the date of creation for your
voucher will be empty. This will not cause any trouble when running
VoSeq. You can safely ignore this message.

Create an index for all the data in your database:

.. code:: shell

    make index

If you kept your **voucher images** in your local computer or server then
your need to copy them to the correct location in the VoSeq folders:

.. code:: shell

    cp old_voseq/pictures/* VoSeq/voseq/public_interface/static/.

Now copy the thumbnails of those images:

.. code:: shell

    cp old_voseq/pictures/thumbnails/* VoSeq/voseq/public_interface/static/.

If you have your photos in Flickr, then don't worry you don't need to copy any
image file.

Set-up a publicly available web server
======================================

To make VoSeq available to multiple users, you will have to set-up a publicly available web server.
There are several options to do this, for example using nginx and gunicorn (best performance) or
Apache and WSGI (more suitable for hosting multiple websites).

Instructions for how to do this will follow later, but the DigitalOcean tutorials may be of use for now:

`Apache and WSGI `__

`Nginx and Gunicorn `__

Administrate the server
=======================

Optionally if you want to add items/vouchers to your database
interactively, you need to create an administration account. Run the
following command and provide the requested information:

.. code:: shell

    make admin

Create a database index for the simple and advanced search functions. This will speed
up the data retrieval. You need to run it once as soon as you deploy VoSeq to the server:

.. code:: shell

    make index

Some features of VoSeq need to be run periodically
--------------------------------------------------
You can setup cronjobs to execute some commands once a day or every 2 hours depending on your needs.

If you remove or add data to VoSeq quite rarely (once a day) you might want to
sync the database index with your real data. In this way, new vouchers or sequences will
be found by VoSeq's search tools.

To update your database index every 24 hours (at 3:00 am) set the following cronjob:

.. code:: shell

    crontab -e

Add the following line, save and exit:

.. code:: shell

    0 3 * * * /path/to/python /path/to/voseq/manage.py update_index --age=24 --remove --settings=voseq.settings.production

If you add and delete data several times a day then you might want to update
your database index more often. Let us try every three hours:

.. code:: shell

    0 */3 * * * /path/to/python /path/to/voseq/manage.py update_index --age=3 --remove --settings=voseq.settings.production

If you installed VoSeq using Vagrant, then your cronjob command with the correct paths should be this:

.. code:: shell

	0 */3 * * * /home/vagrant/.virtualenvs/voseq/bin/python /vagrant/voseq/manage.py update_index --settings=voseq.settings.production

Update some voucher and gene statistics for your installation of VoSeq:

.. code:: shell

    make stats

Deployment of VoSeq
===================
VoSeq comes with a very simple server software (from Django) that you can use
for development and testing purposes. This is the server that starts up when
you use the command ``make serve``.

However, the Django developers warn that you will need to do some extra configuration
if you want VoSeq to start serving data to the users of your lab from your institution
server or commercial servers:

* To serve statics files such as stylesheet and javascript files, you
  need to choose a folder in your sever to be the root folder for such files.
  Open the file ``VoSeq_repo/voseq/voseq/settings/production.py`` and change this
  line so that it points to your server's folder:

.. code:: python

    STATIC_ROOT = "/var/www/VoSeq/static/"

* Do something similar for being able to serve voucher images from your local
  server:

.. code:: python

    MEDIA_ROOT = "/var/www/VoSeq/media/"

You might want to leave it with the default values. It should work (# TODO test).

* If you have installed VoSeq in a commercial server and already bought an Internet
  domain, you need to add it to the ``production.py`` file. Change the following
  line:

.. code:: python

    ALLOWED_HOSTS = [
        '192.168.0.106',  # Your Domain or IP address
    ]

If you don't have a domain like (myawesomedomain.com) then just replace the IP
address for the one of your server.

Before starting up VoSeq, you will need to gather all the static files in the
folders you just specified so they will be available for your users.
Use the following command:

.. code:: shell

    python voseq/manage.py collectstatic --settings=voseq.settings.production

Then start VoSeq using the ``production`` configuration file:

.. code:: shell

    python voseq/manage.py runserver --settings=voseq.settings.production


Upgrade VoSeq's software
========================
If you cloned the VoSeq software you can easily get the new changes by typing the following commands
in a computer terminal or console:

.. code:: shell

    cd /path/to/VoSeq
    git pull origin master


Do the updates to the database structure:

.. code:: shell

    workon voseq_environment
    make migrations


Rebuild the index and start the test server:

.. code:: shell

    make index
    make serve


Database backups
================
You might want to do periodical backups of your VoSeq database. You can follow these instrucctions
for backup data from postgreSQL databases: https://wiki.postgresql.org/wiki/Automated_Backup_on_Linux

Flickr Plugin
=============
VoSeq is able to host all the specimen photos in Flickr. If you have a free
account you can host up to 200 photos. The Pro account allows you hosting
unlimited number of photos for a yearly fee (25 USD).

You need to get `API keys from Flickr `__
and place them in the ``config.json`` configuration file of VoSeq:

* Create and account in Flickr (if you don't own one already)
* Follow the instructions to get an API key and Secret key.
* After submitting you will get your Key and Secret. Write down those keys.
* Using a text editor software, edit the file ``config.json`` by copying your keys in it.

    * For example [these are not real keys and will not work if you use them]::

    .. code:: javascript

        "FLICKR_API_KEY": "2d7f59f9aaa2d5c0a2782d7f5d9083a6",
        "FLICKR_API_SECRET": "ef0def0f3d5f3f15f1"

    * Save and exit.

Thus, every picture that you upload into your VoSeq installation will be uploaded into your Flickr account.
It is necessary to get a flickr token using instructions from the flickrapi .

Lineages
========

GenBank fasta files have the optional field Lineages. You can add lineages in the form:

LINEAGES = {
    # superfamily: lineage from domain Eukaryota to suborder Ditrysia
    "Papilionoidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",
    "Hesperioidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",
    "Hedyloidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",
}

by editing the file `voseq/create_dataset/utils.py`.

Owner

Citation (CITATIONS.md)

# Research papers citing VoSeq

1. Bukontaite, R., Miller, K. B., & Bergsten, J. (**2014**). The utility of 
   CAD in recovering Gondwanan vicariance events and the evolutionary history of 
   Aciliini (Coleoptera: Dytiscidae). *BMC Evolutionary Biology*, 14(1), 5.
   [doi: 10.1186/1471-2148-14-5](http://dx.doi.org/10.1186/1471-2148-14-5)
   
1. Bukontaite R, Ranarilalatiana T, Randriamihaja JH, Bergsten J (**2015**).
   In or Out-of-Madagascar?—Colonization Patterns for Large-Bodied Diving Beetles
   (Coleoptera: Dytiscidae). *PLoS ONE*, 10(3): e0120777.
   [doi: 10.1371/journal.pone.0120777](10.1371/journal.pone.0120777)
   
1. Cally S, Solbès P, Grosso B, Murienne J (**2014**) An occurence records 
   database of French Guiana harvestmen (Arachnida, Opiliones). *Biodiversity 
   Data Journal*, 2: e4244.
   [doi: 10.3897/BDJ.2.e4244](http://dx.doi.org/10.3897/BDJ.2.e4244)

2. Doorenweerd C, van Nieukerken EJ, Menken SBJ (**2015**) A Global Phylogeny of
   Leafmining *Ectoedemia* Moths (Lepidoptera: Nepticulidae): Exploring Host
   Plant Family Shifts and Allopatry as Drivers of Speciation. *PLoS ONE* 10(3):
   e0119586. [doi: 10.1371/journal.pone.0119586](http://dx.doi.org/10.1371/journal.pone.0119586) 

1. Heikkilä, M. (**2014**). Systematizing morphology: a total evidence 
   approach to ditrysian phylogenetics (Lepidoptera). University of Helsinki. 
   PhD thesis.
   
1. Heikkilä, M., Mutanen, M., Kekkonen, M., & Kaila, L. (**2013**). Morphology 
   reinforces proposed molecular phylogenetic affinities: a revised 
   classification for Gelechioidea (Lepidoptera). *Cladistics*, 30(6), 563–589.
   [doi: 10.1111/cla.12064](http://dx.doi.org/10.1111/cla.12064)
   
1. Heikkilä, M., Mutanen, M., Wahlberg, N., Sihvonen, P., & Kaila, L. (**2015**).
   Elusive ditrysian phylogeny: an account of combining systematized morphology
   with molecular data (Lepidoptera). *BMC evolutionary biology*, 15(1), 260.
   [doi: 10.1186/s12862-015-0520-0](http://dx.doi.org/10.1186/s12862-015-0520-0)
   
1. Hoyt, C. A. (**2014**). The Spotless Comma (*Polygonia haroldii*): a new species 
   for the United States.  *News of the Lepidopterists' Society*, 56(1): 14-15, 33.
   
1. Kaila, L., Epstein, M. E., Heikkilä, M., & Mutanen, M. (**2013**). The
   assignment of Prodidactidae to Hyblaeoidea, with remarks on Thyridoidea
   (Lepidoptera). *Zootaxa*, 3682(3), 485-494. 
   
1. Kaminski, L. A., Soares, G. R., Seraphim, N., Wahlberg, N., Marini-Filho, 
   O. J., & Freitas, A. V. Natural history and systematic position of
   *Rhetus belphegor* (n. comb.) (Lepidoptera: Riodinidae), an endangered butterfly 
   with narrow distribution in Southeast Brazil. *Journal of Insect Conservation*,
   19(6): 1141-1151. 
   [doi: 10.1007/s10841-015-9829-7](http://dx.doi.org/10.1007/s10841-015-9829-7)
   
1. Karsholt, O., Mutanen, M., Lee, S., & Kaila, L. (**2013**). A molecular 
   analysis of the Gelechiidae (Lepidoptera, Gelechioidea) with an 
   interpretative grouping of its taxa. *Systematic Entomology*, 38(2), 
   334-348.
   [doi: 10.1111/syen.12006](http://dx.doi.org/10.1111/syen.12006)
   
2. Kristensen, N. P., Hilton, D. J., Kallies, A., Milla, L., Rota, J., Wahlberg, N.,
   Wilcox, S. A., Glatz, R. V., Young, D. A., Cocking, G., Edwards, T.,
   Gibbs, G. W. & Halsey, M. (**2015**). A new extant family of primitive moths
   from Kangaroo Island, Australia, and its significance for understanding
   early Lepidoptera evolution. *Systematic Entomology*, 40: 5–16. 
   [doi: 10.1111/syen.12115](http://dx.doi.org/10.1111/syen.12115)
   
2. Malm, T., Johanson, K. A., & Wahlberg, N. (**2013**). The evolutionary 
   history of Trichoptera (Insecta): A case of successful adaptation to life in 
   freshwater. *Systematic Entomology*, 38(3), 459-473. 
   [doi: 10.1016/j.ympev.2012.09.005](http://dx.doi.org/10.1016/j.ympev.2012.09.005)
   
3. Malm, T., & Nyman, T. (**2015**). Phylogeny of the symphytan grade of 
   Hymenoptera: new pieces into the old jigsaw (fly) puzzle. *Cladistics*,
   31(1), 1–17.
   [doi: 10.1111/cla.12069](http://dx.doi.org/10.1111/cla.12069)
   
3. Matos-Maraví, P., Águila, R. N., Peña, C., Miller, J. Y., Sourakov, A., 
   & Wahlberg, N. (**2014**). Causes of endemic radiation in the Caribbean: 
   evidence from the historical biogeography and diversification of the 
   butterfly genus *Calisto* (Nymphalidae: Satyrinae: Satyrini). *BMC 
   Evolutionary Biology*, 14(1), 199. 
   
3. Matos-Maraví, P. F., Peña, C., Willmott, K. R., Freitas, A. V., 
   & Wahlberg, N. (**2013**). Systematics and evolutionary history of 
   butterflies in the *Taygetis clade* (Nymphalidae: Satyrinae: Euptychiina):
   Towards a  better understanding of Neotropical biogeography. *Molecular 
   phylogenetics and evolution*, 66(1), 54-68.
   [doi: 10.1016/j.ympev.2012.09.005](http://dx.doi.org/10.1016/j.ympev.2012.09.005)
   
3. Pellinen, M. J., & Wahlberg, N. (**2015**). A new species of *Niganda* Moore,
   1879 from Thailand, with descriptions of variation in male genitalia and 
   female facies of *N. radialis* Moore (Lepidoptera: Notodontidae, Ceirinae).
   *Zootaxa*, 4033(1): 94-102.
   [doi: 10.11646/zootaxa.4033.1.4](http://dx.doi.org/10.11646/zootaxa.4033.1.4)
  
3. Peña, C., Witthauer, H., Klečková, I., Fric, Z. & Wahlberg, N. (**2015**). Adaptive
   Radiations in Butterflies: Evolutionary History of the Genus Erebia (Nymphalidae:
   Satyrinae). *Biological Journal of the Linnean Society*,
   [doi: 10.1111/bij.12597](http://dx.doi.org/10.1111/bij.12597)

4. Müller, C. J., Matos‐Maraví, P. F., & Beheregaray, L. B. (**2013**). Delving 
   into *Delias* Hübner (Lepidoptera: Pieridae): fine‐scale biogeography, 
   phylogenetics and systematics of the world's largest butterfly genus. 
   *Journal of Biogeography*, 40(5), 881-893.
   [doi: 10.1111/jbi.12040](http://dx.doi.org/10.1111/jbi.12040)
   
4. Rey Fraile, I. (**2014**). La conservación del patrimonio genético: 
   Colecciones de ADN y tejidos. UNIVERSIDAD COMPLUTENSE DE MADRID. PhD thesis.
  
4. Rota, J., & Miller, S. E. (**2013**). A new genus of metalmark moths 
   (Lepidoptera, Choreutidae) with Afrotropical and Australasian distribution.
   ZooKeys, (355), 29.
  
1. Sorger, D. M. (**2015**). On ants, islands and evolution. NORTH CAROLINA
   STATE UNIVERSITY. PhD thesis.

1. Stigenberg, J., Boring, C. A., & Ronquist, F. (**2015**). Phylogeny of the 
   parasitic wasp subfamily Euphorinae (Braconidae) and evolution of its host 
   preferences. *Systematic Entomology*, 40(3): 570-591. 
   [doi: 10.1111/syen.12122](http://dx.doi.org/10.1111/syen.12122)
   
1. Talaga, S., Murienne, J., Dejean, A., & Leroy, C. (**2015**). Online database
   for mosquito (Diptera, Culicidae) occurrence records in French Guiana. 
   *ZooKeys*, 532: 107-115. 
   [doi: 10.3897/zookeys.532.6176](http://dx.doi.org/10.3897/zookeys.532.6176)

1. Toth, J. P., Bereczki, J., Varga, Z., Rota, J., Sramko, G., & Wahlberg, 
   N. (**2014**). Relationships within the *Melitaea phoebe* species group 
   (Lepidoptera: Nymphalidae): new insights from molecular and morphometric 
   information. *Systematic Entomology*, 39(4), 749-757. 
   [doi: 10.1111/syen.12083](http://dx.doi.org/10.1111/syen.12083)
   
5. Wahlberg, E., & Johanson, K. A. (**2014**). The age, ancestral distribution
   and radiation of *Chimarra* (Trichoptera: Philopotamidae) using  molecular
   methods. *Molecular phylogenetics and evolution*, 79, 433-442.
   [doi: 10.1016/j.ympev.2014.06.023](http://dx.doi.org/10.1016/j.ympev.2014.06.023)
   
5. Wahlberg, N., Rota, J., Braby, M. F., Pierce, N. E., & Wheat,  C. W.
   (**2014**). Revised systematics and higher classification of pierid 
   butterflies (Lepidoptera: Pieridae) based on molecular data. *Zoologica 
   Scripta*, 43(6), 641-650. 
   
5. Wilson, J. J., Sing, K. W., & Sofian-Azirun, M. (**2013**). Building a DNA 
   Barcode Reference Library for the True Butterflies (Lepidoptera) of 
   Peninsula Malaysia: What about the Subspecies?. *PLOS ONE*, 8(11), e79969.
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6. Zaspel, J. M., Weller, S. J., Wardwell, C. T., Zahiri, R., & Wahlberg,  N.
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