phylip.py

from Bio import AlignIO


def column(alignment):
    '''Generator for getting list of characters in each column in the alignment'''
    for i in range(alignment.get_alignment_length()):
        c = []

        for record in alignment:
            c.append(record.seq[i])

        yield c


alignment = AlignIO.read(open("input.txt"), "phylip")  # open phylip file
names = [record.id for record in alignment]  # save IDs of the alignments

list2 = []  # list for columns with "-"
list3 = []  # list for columns without "-"

# Get each column in the alignment
# if it contains "-" add column to list2 otherwise to list3
for c in column(alignment):
    if "-" in c:
        list2.append(c)
    else:
        list3.append(c)

# write columns with "-" to file list2.txt
with open("list2.txt", "w") as outfile:
    for i, line in enumerate(zip(*list2)):
        outfile.write(names[i]+" "+"".join(line)+"\n")

# write columns without "-" to file list3.txt
with open("list3.txt", "w") as outfile:
    for i, line in enumerate(zip(*list3)):
        outfile.write(names[i]+" "+"".join(line)+"\n")

Answer on biostars question: https://www.biostars.org/p/326044