If you need more control over your tree images, you can program how the tree is rendered using ETE (Python language)

A very very simple example that associates node features with node size and color would look like this:

from ete2 import Tree, faces
import colorsys
import random

def hls2hex(h, l, s):
    ''' Converts from HLS to RGB '''
    return '#%02x%02x%02x' %tuple(map(lambda x: int(x*255), 
                                      colorsys.hls_to_rgb(h, l, s)))
def get_color(h=None, s=0.5, l=0.5):
    ''' Returns a RGB color code with the specific Hue, Saturation and
    lightness. Otherwise, it returns a random color'''
    if not h:
        h = random.random()
    return hls2hex(h, l, s)

def my_layout(node):
    """ This function set the rules that control how nodes are drawn"""
    value = tax2size.getnode.name, None)
    if value is not None:

        # generate a gradient on color lightness for 0.3 to 0.8. A
        # assume value is in the (0,1) range.
        gradient = 0.3 + (float(value)/100)/2

        # Set node size and color based on the dictionary of user
        # values
        color = get_color(h=0.9, l=gradient)
        node.img_style["size"] = 20 + value
        node.img_style["fgcolor"] = color
        node.img_style["line_type"] = 1

        # Text labels can also be added to the image
        faces.add_face_to_node(faces.TextFace(" (%s) " %node.name), \
                                   node=node, column=0, aligned=True)

        faces.add_face_to_node(faces.TextFace("value: %s" %value), \
                                   node=node, column=1, aligned=True)
    else:
        node.img_style["size"] = 0

# Loads the example tree
t = Tree("(((9606,9844),99287),(9823,9913));")

# Loads the example values associated to leaf nodes
tax2size = {
    "9606": 100, "9823": 80,  "9844": 60,  "9913": 40,  "99287": 20  }

t.show(my_layout)
t.render("gradient.png", my_layout)

fullsize

I would use iTOL for that. I am not sure if it can do a color gradient, but it has several different ways of visualizing data onto a phylogenetic tree.

If you happen to be tackling metagenomic data (I am not sure), MEGAN will be of much help, in the task of actually sorting out the phylogenetic relationships, even of unknown taxa.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800929/

Similar plots as posted by jhc can be created directly in the software.

excerpt:

In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequenceconservation of the sequence conservation of the sequence

If you can convert those taxids to scientific names of species and use a comma-separated table, then you can use my PHYLOmap to visualise phylogenetic tree (which links up with ITOL).

Format the data as table.csv given on page 2.

Best Wishes,
Umer