The Protocol Informatics Framework
Written by Marshall Beddoe <[email protected]>
Copyright (c) 2004 Baseline Research
----

Wired Article:
https://www.wired.com/2004/10/genome-model-applied-to-software/

Overview:

The Protocol Informatics project is a software framework that allows for
advanced sequence and protocol stream analysis by utilizing bioinformatics
algorithms. The sole purpose of this software is to identify protocol fields in
unknown or poorly documented network protocol formats. The algorithms that are
utilized perform comparative analysis on a series of samples to better
understand the underlying structure of the otherwise random-looking data. The
PI framework was designed for experimentation through the use of a widget-based
component set.

Requirements:

Python >= 2.3.4     http://www.python.org
Numerical Python    http://www.stsci.edu/resources/software_hardware/numarray
Pyrex               http://www.cosc.canterbury.ac.nz/~greg/python/Pyrex/
Pcapy               http://oss.coresecurity.com/projects/pcapy.html
Pydot               http://dkbza.org/pydot.html

This software has been tested and works correctly under:
    - OpenBSD
    - FreeBSD
    - Linux
    - MacOSX

Example usage: Analyzing the ICMP protocol

ICMP is a simple fixed length protocol.
Let's use the PI framework to discover the format.

Step 1: Gather 100 ICMP packets using tcpdump

# tcpdump -s 42 -c 100 -nl -w icmp.dump icmp

Step 2: Run dump through PI prototype

# ./main.py -g -p ./icmp.dump

Protocol Informatics Prototype (v0.01 beta)
Written by Marshall Beddoe <[email protected]>
Copyright (c) 2004 Baseline Research

Found 100 unique sequences in '../dumps/icmp.out'
Creating distance matrix .. complete
Creating phylogenetic tree .. complete

Discovered 1 clusters using a weight of 1.00
Performing multiple alignment on cluster 1 .. complete

Output of cluster 1
0097 x08 x00 xad x4b x05 xbe x00 x60
0039 x08 x00 x30 x54 x05 xbe x00 x26
0026 x08 x00 xf7 xb2 x05 xbe x00 x19
0015 x08 x00 x01 xdb x05 xbe x00 x0e
0048 x08 x00 x4f xdf x05 xbe x00 x2f
0040 x08 x00 xf8 xa4 x05 xbe x00 x27
0077 x08 x00 xe8 x28 x05 xbe x00 x4c
0017 x08 x00 xe8 x6c x05 xbe x00 x10
0027 x08 x00 xc3 xa9 x05 xbe x00 x1a
0087 x08 x00 xdd xc1 x05 xbe x00 x56
0081 x08 x00 x88 x42 x05 xbe x00 x50
0058 x08 x00 xb0 x42 x05 xbe x00 x39
0013 x08 x00 x3e x38 x05 xbe x00
0067 x08 x00 x99 x36 x05 xbe x00 x42
0055 x08 x00 x0f x56 x05 xbe x00 x36
0004 x08 x00 xe6 xda x05 xbe x00 x03
0028 x08 x00 x83 xd9 x05 xbe x00 x1b
0095 x08 x00 xc1 xd9 x05 xbe x00 x5e
0075 x08 x00 x3a x63 x05 xbe x00 x4a
0053 x08 x00 x6d x2a x05 xbe x00 x34
0021 x08 x00 x6d x8d x05 xbe x00 x14
0088 x08 x00 xa8 x07 x05 xbe x00 x57
0005 x08 x00 xa8 x8a x05 xbe x00 x04
0080 x08 x00 xa8 x62 x05 xbe x00 x4f
0023 x08 x00 x3f x18 x05 xbe x00 x16
0002 x08 x00 x3f x65 x05 xbe x00 x01
0074 x08 x00 x3f xc2 x05 xbe x00 x49
0030 x08 x00 x3f x15 x05 xbe x00 x1d
0044 x08 x00 xcc xc2 x05 xbe x00 x2b
0078 x08 x00 xcc x8a x05 xbe x00 x4d
0071 x08 x00 xd8 x18 x05 xbe x00 x46
0035 x08 x00 x9a xfd x05 xbe x00 x22
0001 x08 x00 x69 xf9 x05 xbe x00 x00
0034 x08 x00 xc5 x9e x05 xbe x00 x21
0031 x08 x00 x38 x00 x05 xbe x00 x1e
0092 x08 x00 x38 x4c x05 xbe x00 x5b
0100 x08 x00 x2b x1a x05 xbe x00 x63
0049 x08 x00 x15 x1d x05 xbe x00 x30
0008 x08 x00 x2f x64 x05 xbe x00 x07
0089 x08 x00 x80 xe5 x05 xbe x00 x58
0096 x08 x00 xb2 xb0 x05 xbe x00 x5f
0079 x08 x00 xc2 xae x05 xbe x00 x4e
0057 x08 x00 xc2 x79 x05 xbe x00 x38
0046 x08 x00 x77 x7a x05 xbe x00 x2d
0018 x08 x00 xbb xce x05 xbe x00 x11
0025 x08 x00 xfe xaa x05 xbe x00 x18
0068 x08 x00 x50 xe3 x05 xbe x00 x43
0065 x08 x00 xe0 xb7 x05 xbe x00 x40
0011 x08 x00 x8d xd6 x05 xbe x00
0029 x08 x00 x7c xf3 x05 xbe x00 x1c
0033 x08 x00 xef xf3 x05 xbe x00
0069 x08 x00 x25 x6b x05 xbe x00 x44
0083 x08 x00 x25 xff x05 xbe x00 x52
0099 x08 x00 x56 x99 x05 xbe x00 x62
0061 x08 x00 x33 x81 x05 xbe x00 x3c
0050 x08 x00 xe9 xba x05 xbe x00 x31
0042 x08 x00 xb3 x49 x05 xbe x00 x29
0059 x08 x00 x81 x4e x05 xbe x00 x3a
0098 x08 x00 x81 xad x05 xbe x00 x61
0091 x08 x00 x42 xa0 x05 xbe x00 x5a
0054 x08 x00 x42 xd8 x05 xbe x00 x35
0037 x08 x00 x4c xe8 x05 xbe x00 x24
0041 x08 x00 xeb x4d x05 xbe x00 x28
0086 x08 x00 xe4 x53 x05 xbe x00 x55
0006 x08 x00 x71 x7b x05 xbe x00 x05
0012 x08 x00 x63 x7b x05 xbe x00
0070 x08 x00 xee x7d x05 xbe x00 x45
0051 x08 x00 xc8 x57 x05 xbe x00 x32
0066 x08 x00 xb4 x3c x05 xbe x00 x41
0014 x08 x00 x2c x26 x05 xbe x00
0062 x08 x00 x2c x7c x05 xbe x00 x3d
0016 x08 x00 xed x8e x05 xbe x00 x0f
0007 x08 x00 x47 x3d x05 xbe x00 x06
0073 x08 x00 x5e x72 x05 xbe x00 x48
0052 x08 x00 x9e x06 x05 xbe x00 x33
0072 x08 x00 x9e x9d x05 xbe x00 x47
0036 x08 x00 x6f x6e x05 xbe x00 x23
0060 x08 x00 x6c xc6 x05 xbe x00 x3b
0045 x08 x00 xa2 xf5 x05 xbe x00 x2c
0085 x08 x00 x00 x47 x05 xbe x00 x54
0076 x08 x00 x14 x85 x05 xbe x00 x4b
0020 x08 x00 xa0 x85 x05 xbe x00 x13
0019 x08 x00 xa6 x2c x05 xbe x00 x12
0003 x08 x00 x14 x2c x05 xbe x00 x02
0022 x08 x00 x44 x8c x05 xbe x00 x15
0082 x08 x00 x5d xe0 x05 xbe x00 x51
0009 x08 x00 xfc x41 x05 xbe x00 x08
0084 x08 x00     x35 x05 xbe x00 x53
0032 x08 x00 x0e x17 x05 xbe x00 x1f
0056 x08 x00 xe5     x05 xbe x00 x37
0043 x08 x00 xa1 xde x05 xbe x00 x2a
0094 x08 x00 x03 x92 x05 xbe x00 x5d
0047 x08 x00 x55 x83 x05 xbe x00 x2e
0090 x08 x00 x55 x94 x05 xbe x00 x59
0064 x08 x00     x8f x05 xbe x00 x3f
0093 x08 x00     xb6 x05 xbe x00 x5c
0010 x08 x00 xd1 xb6 x05 xbe x00
0024 x08 x00 x11 x8f x05 xbe x00 x17
0063 x08 x00 x11 x04 x05 xbe x00 x3e
0038 x08 x00 x37 x3b x05 xbe x00 x25
DT   BBB ZZZ BBB BBB BBB BBB ZZZ AAA
MT   000 000 081 089 000 000 000 100

Ungapped Consensus:
CONS x08 x00 x3f x18 x05 xbe x00 ???
DT   BBB ZZZ BBB BBB BBB BBB ZZZ AAA
MT   000 000 081 089 000 000 000 100

Step 3: Analyze Consensus Sequence

Pay attention to datatype composition and mutation rate.

Offset 0: Binary data, 0% mutation rate
Offset 1: Zeroed data, 0% mutation rate
Offset 2: Binary data, 81% mutation rate
Offset 3: Binary data, 89% mutation rate
Offset 4: Binary data, 0% mutation rate
Offset 5: Binary data, 0% mutation rate
Offset 6: Zeroed data, 0% mutation rate
Offset 7: ASCII data, 100% mutation rate

Using this information we can construct the structure of the format:

[ 1 byte ] [ 1 byte ] [ 2 byte ] [ 2 byte ] [ 1 byte ] [ 1 byte ]

The real format of an ICMP message:

[ 1 byte ] [ 1 byte ] [ 2 byte ] [ 2 byte ] [ 2 byte ]

The reason PI made the mistake in identifying the last field was due to the
fact that the last field in an ICMP packet is a 16 bit sequence identifier.
We only gathered 100 packets therefore the greatest significant byte never
changed as the field incremented.

Therefore, it is very important to gather data efficiently as PI is only as
good as the data that is fed to it.