diff --git a/readseq.py b/readseqs.py
similarity index 100%
rename from readseq.py
rename to readseqs.py
diff --git a/tree.py b/tree.py
deleted file mode 100644
index f210c20..0000000
--- a/tree.py
+++ /dev/null
@@ -1,140 +0,0 @@
-import random
-
-class node(object):
-    def __init__(self, ndnum):      # initialization function
-        self.rsib = None            # right sibling
-        self.lchild = None          # left child
-        self.par = None             # parent node
-        self.number = ndnum         # node number
-        self.edgelen = 0.0          # branch length
-        self.height = 0.0           # height above root
-        self.deep = False           # True if this node resulted from a deep coalescence
-        self.descendants = set([ndnum])    # set containing descendant leaf set
-
-def joinRandomPair(node_list, next_node_number, is_deep_coalescence):
-    # pick first of two lineages to join and delete from node_list
-    i = random.randint(1, len(node_list))
-    ndi = node_list[i-1]
-    del node_list[i-1]
-
-    # pick second of two lineages to join and delete from node_list
-    j = random.randint(1, len(node_list))
-    ndj = node_list[j-1]
-    del node_list[j-1]
-
-    # join selected nodes and add ancestor to node_list
-    ancnd = node(next_node_number)
-    ancnd.deep = is_deep_coalescence
-    ancnd.lchild = ndi
-    ancnd.descendants = set()
-    ancnd.descendants |= ndi.descendants
-    ancnd.descendants |= ndj.descendants
-    ndi.rsib = ndj
-    ndi.par = ancnd
-    ndj.par = ancnd
-    node_list.append(ancnd)
-
-    return node_list
-
-def joinSpecificPair(node_list, i, j, next_node_number, is_deep_coalescence):
-    assert j != i
-
-    ndi = None
-    for k,nd in enumerate(node_list):
-        if nd.number == i:
-            ndi = node_list.pop(k)
-    assert ndi is not None
-
-    ndj = None
-    for k,nd in enumerate(node_list):
-        if nd.number == j:
-            ndj = node_list.pop(k)
-    assert ndj is not None
-
-    # join selected nodes and add ancestor to node_list
-    ancnd = node(next_node_number)
-    ancnd.deep = is_deep_coalescence
-    ancnd.lchild = ndi
-    ancnd.descendants = set()
-    ancnd.descendants |= ndi.descendants
-    ancnd.descendants |= ndj.descendants
-    ndi.rsib = ndj
-    ndi.par = ancnd
-    ndj.par = ancnd
-    node_list.append(ancnd)
-
-    return node_list
-
-def getPreorder(nd, start = True):
-    global _preorder
-    if start:
-        _preorder = []
-
-    _preorder.append(nd)
-
-    if nd.lchild:
-        getPreorder(nd.lchild, False)
-
-    if nd.rsib:
-        getPreorder(nd.rsib, False)
-
-    return _preorder
-
-def flipAllNodesAbove(root):
-    node_list = getPreorder(root)
-    for nd in node_list:
-        if nd.lchild:
-            lc = nd.lchild
-            rc = lc.rsib
-            nd.lchild = rc
-            assert rc.rsib is None
-            rc.rsib = lc
-            lc.rsib = None
-
-def makeNewick(nd, brlen_scaler = 1.0, start = True):
-    global _newick
-    global _TL
-    if start:
-        _newick = ''
-        _TL = 0.0
-
-    if nd.lchild:
-        _newick += '('
-        makeNewick(nd.lchild, brlen_scaler, False)
-    else:
-        blen = nd.edgelen*brlen_scaler
-        _TL += blen
-        _newick += '%d:%.5f' % (nd.number, blen)
-
-    if nd.rsib:
-        _newick += ','
-        makeNewick(nd.rsib, brlen_scaler, False)
-    elif nd.par is not None:
-        blen = nd.par.edgelen*brlen_scaler
-        _TL += blen
-        _newick += '):%.5f' % blen
-
-    return _newick, _TL
-
-def calcActualHeight(root):
-    h = 0.0
-    nd = root
-    while nd.lchild:
-        nd = nd.lchild
-        h += nd.edgelen
-    return h
-
-def sumEdgeLengths(root):
-    sum_edge_lengths = 0.0
-    pre = getPreorder(root)
-    for nd in pre:
-        sum_edge_lengths += nd.edgelen
-    return sum_edge_lengths
-
-def countDeepCoalescences(root):
-    n = 0
-    preorder = getPreorder(root)
-    for nd in preorder:
-        if nd.deep:
-            n += 1
-    return n