Align and visualize multiple (mitochondria) nucleotide sequence (.fasta) files

## Background

Looking at genetic alignments is a very important part of molecular biology. The human eye can pick up patterns on a small scale, then we can program the computer to pick out similar patterns on a much larger scale.

Making alignments creates an indexed location for each nucleotide in a fasta file. In turn, this will allow downstream processing like determining the distance between two sequences.

## Aim

Align the 9 .fasta files in this folder:

[mitolin/data/gen/nguyen_nc_2018/20190702-fastas-on-hpc/1739/20lines/](https://github.com/deepcelllineage/mitolin/tree/master/data/gen/nguyen_nc_2018/20190702-fastas-on-hpc/1739/20lines)

Related to [issue 5](https://github.com/deepcelllineage/mitolin/issues/5)
Related to [issue 1 fluHA](https://github.com/deepcelllineage/fluHA/issues/1)

## Method

You can start with Blast or Muscle. Muscle will generate a sequence distance score that can be used to make a lineage tree (aka dendogram/hierarchical clusters).

Wikipedia has a list of alignment visualization software [here](https://en.wikipedia.org/wiki/List_of_alignment_visualization_software).

## Document your work

Please fork & clone this repo. Check out a branch for your work, then push and make a PR for us to merge your note and files.

Add a note (can be .md or .ipynb) with your solution to [mitolin/nb](https://github.com/deepcelllineage/mitolin/tree/master/nb).

Your note should be named as follows:

- DATE-issue#-shortdescription.ext

e.g.:

- 20190701-i02-extract-chrM-fa.md

## Questions?

Please put questions related to this issue in this issue thread. If you want a quick response, post a link to your comment in this thread to Slack #deepcelllineage or DM @Deena. To join Slack enter your email address [here](http://bit.ly/JoinSlackFastaiSFbay). For questions NOT specifically related to this issue, get in touch through any of the communication methods listed in [DCL's overview README](https://github.com/deepcelllineage/overview/blob/master/README.md).

Start by inspecting the nine FASTA files in data/gen/nguyen_nc_2018/20190702-fastas-on-hpc/1739/20lines/ and the existing notebooks in nb. Compare the suggested Muscle or Blast approaches, align the sequences, and visualize the result. Done means a dated issue-7 note in nb documents the method and includes the alignment and visualization outputs.

Written by the indexing model from the issue text.