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#include "muscle.h"
#include "msa.h"
#include "textfile.h"
#include "tree.h"
void DoMakeTree()
{
if (g_pstrInFileName == 0 || g_pstrOutFileName == 0)
Quit("-maketree requires -in <msa> and -out <treefile>");
SetStartTime();
SetSeqWeightMethod(g_SeqWeight1);
TextFile MSAFile(g_pstrInFileName);
MSA msa;
msa.FromFile(MSAFile);
unsigned uSeqCount = msa.GetSeqCount();
MSA::SetIdCount(uSeqCount);
// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
msa.SetSeqId(uSeqIndex, uSeqIndex);
SetMuscleInputMSA(msa);
Progress("%u sequences", uSeqCount);
Tree tree;
TreeFromMSA(msa, tree, g_Cluster2, g_Distance2, g_Root2);
TextFile TreeFile(g_pstrOutFileName, true);
tree.ToFile(TreeFile);
Progress("Tree created");
}
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