$cat file_1

name_of_sequence    C    other_information
name_of_sequence    C    other_information
name_of_sequence    C    other_information
name_of_sequence    D    other_information
...

$cat file_2

name_of_sequence    B    other_information
name_of_sequence    C    other_information
name_of_sequence    C    other_information
name_of_sequence    C    other_information
...

$cat file_3

name_of_sequence    A    other_information
name_of_sequence    A    other_information
name_of_sequence    A    other_information
name_of_sequence    A    other_information
...

$cat .csv/.tsv output:

taxa     A    B    C    D    E
File_1   0    0    3    8    1
File_2   0    1    3    2    9
File_3   7    3    9    0    6

import sys
import csv

names = set()

files = {}

for file_name in sys.argv[1:]:
    b = files.setdefault(file_name, {})
    with open(file_name) as fp:
        for line in fp:
            x = line.strip().split()
            names.add(x[1])
            b.setdefault(x[1], [0])[0] += 1

names = sorted(list(names))
grid = []
top_line = ['taxa']
grid.append(top_line)
for name in names:
    top_line.append(name)
for file_name in sys.argv[1:]:
    data = files[file_name]
    line = [file_name]
    grid.append(line)
    for name in names:
        line.append(data.get(name, [0])[0])

with open('out.csv', 'w') as fp:
    writer = csv.writer(fp)
    writer.writerows(grid)