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# Seqsim Simple Alignment Simulation Example

Section author: Julia Goodrich

This is a very simple example of how to use the `seqsim` module to simulate an alignment for a tree starting with a random sequence and substitution rate matrix (q). The rate matrix gives the rate constant of going from one character in the sequence to another character in the sequence, the Q matrix determines the rate of change of the sequence.

First we will perform the necessary imports:

- `Rates` is an object that stores the rate matrix data, it can also be used

    to generate a random rate matrix given an `Alphabet`.

- `DnaUsage` is a `Usage` object that stores the usage of each nucleotide.

- `DnaPairs` is an Alphabet it stores the DNA pairs (AA,AT,AC,...), it can

    be passed into the `Rates` object, defining the rate matrix pairs for DNA.

- `DNA` is a `MolType` object for DNA.

- `RangeNode` is the main `seqsim` Node object, it allows for the easy

    evolution of sequences.

- `DndParser` is a parser for a newick format tree.

    >>> from cogent.seqsim.usage import Rates, DnaUsage
    >>> from cogent.core.usage import DnaPairs
    >>> from cogent.core.moltype import DNA
    >>> from cogent.core.alignment import Alignment
    >>> from cogent.seqsim.tree import RangeNode
    >>> from cogent.parse.tree import DndParser

Now, lets specify a 4 taxon tree:

    >>> t = DndParser('(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);',
    ... constructor = RangeNode)

To generate a random DNA sequence, we first specify nucleotide frequencies with the `DnaUsage` object. Then we create a random DNA sequence that is five bases long.

    >>> u = DnaUsage({'A':0.5,'T':0.2,'C':0.15,'G':0.25})
    >>> s = DNA.ModelSeq(u.randomIndices(5))
    >>> q = Rates.random(DnaPairs)

Set q at the base of the tree and propagate it to all nodes in the tree,

    >>> t.Q = q
    >>> t.propagateAttr('Q')

Set a P matrix (probability matrix) from every Q matrix on each node:
  P(t) = e^(Qt),

    >>> t.assignP()

Use `evolve` to evolve sequences for each tip, Note: must evolve sequence data, not sequence object itself (for speed)

Build alignment,

    >>> seqs = {}
    >>> for n in t.tips():
    ...     seqs[n.Name] = DNA.ModelSeq(n.Sequence)
    >>> aln = Alignment(seqs)

The result is a Cogent `Alignment` object, which can be used the same way as any other alignment object.

`evolveSeqs` can be used instead of evolve to evolve multiple sequences according to the same tree (can model either different genes, or different rate categories within a gene that you then combine, etc...),

    >>> from numpy import concatenate

First you need to use `assignPs` to assign the proper P matricies given rates:

    >>> t.assignPs([.5, .75, 1])

There needs to be the same number of random sequences as there are rate catigories so we create a list of 3 random sequences,

    >>> s = [DNA.ModelSeq(u.randomIndices(5))._data for i in range(0,3)]

Then use `evolveSeqs` to evolve a sequence for every tip with every rate.

    >>> t.evolveSeqs(s)

Now to concatenate the sequences,

    >>> seqs = {}
    >>> for n in t.tips():
    ...     for s in n.Sequences:
    ...         seqs[n.Name] = DNA.ModelSeq(concatenate(tuple(n.Sequences)))
    >>> aln = Alignment(seqs)

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