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BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program. BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data. The script works in UNIX-like environments (e.g., LINUX, MacOS, Windows Subsystem for LINUX).

59 BASIC BIOLOGICAL SCIENCES

Hybrid and concatenated coding applications.

Results of a study to evaluate the performance and implementation complexity of a concatenated and a hybrid coding system for moderate-speed deep-space applications. It is shown that with a total complexity of less than three times that of the basic Viterbi decoder, concatenated coding improves a constraint length 8 rate 1/3 Viterbi decoding system by 1.1 and 2.6 dB at bit error probabilities of 0.0001 and one hundred millionth, respectively. With a somewhat greater total complexity, the hybrid coding system is shown to obtain a 0.9-dB computational performance improvement over the basic rate 1/3 sequential decoding system. Although substantial, these complexities are much less than those required to achieve the same performances with more complex Viterbi or sequential decoder systems.

Hofman, L. B.

Performance of concatenated codes for deep space missions

Computer simulation results are presented on the performance of convolutional codes of constraint lengths 7 and 10 concatenated with the (255, 223) Reed-Solomon code (a proposed NASA standard). These results indicate that as much as 0.8 dB can be gained by concatenating this Reed-Solomon code with a (10, 1/3) convolutional code, instead of the (7, 1/2) code currently used by the DSN.

Butman, S. A.

An experimental study of the concatenated Reed-Solomon/Viterbi channel coding system performance and its impact on space communications

The need for efficient space communication at very low bit error probabilities to the specification and implementation of a concatenated coding system using an interleaved Reed-Solomon code as the outer code and a Viterbi-decoded convolutional code as the inner code. Experimental results of this channel coding system are presented under an emulated S-band uplink and X-band downlink two-way space communication channel, where both uplink and downlink have strong carrier power. This work was performed under the NASA End-to-End Data Systems program at JPL. Test results verify that at a bit error probability of 10 to the -6 power or less, this concatenated coding system does provide a coding gain of 2.5 dB or more over the Viterbi-decoded convolutional-only coding system. These tests also show that a desirable interleaving depth for the Reed-Solomon outer code is 8 or more. The impact of this "virtually" error-free space communication link on the transmission of images is discussed and examples of simulation results are given.

Liu, K. Y.

On the error statistics of Viterbi decoding and the performance of concatenated codes

Computer simulation results are presented on the performance of convolutional codes of constraint lengths 7 and 10 concatenated with the (255, 223) Reed-Solomon code (a proposed NASA standard). These results indicate that as much as 0.8 dB can be gained by concatenating this Reed-Solomon code with a (10, 1/3) convolutional code, instead of the (7, 1/2) code currently used by the DSN. A mathematical model of Viterbi decoder burst-error statistics is developed and is validated through additional computer simulations.

Miller, R. L.

The effects of receiver tracking phase error on the performance of the concatenated Reed-Solomon Viterbi channel coding system

In connection with attempts to achieve very low error probabilities, Odenwalder (1970) proposed a concatenated coding system using the Viterbi-decoded convolutional codes as the inner code and Reed-Solomon (RS) codes as the outer code. Analytical and experimental results are presented concerning the effects of the receiver tracking phase error on the performance of the concatenated RS/Viterbi channel coding system. On the basis of these results it is concluded that certain problems regarding communication operations on deep-space missions can be alleviated by employing the RS/Viterbi coding system. In one-way communication, an employment of RS/Viterbi coding will also provide greater data protection than the Viterbi-decoded convolutional-only coding system.

Liu, K. Y.

Performance of concatenated Reed-Solomon/Viterbi channel coding

The concatenated Reed-Solomon (RS)/Viterbi coding system is reviewed. The performance of the system is analyzed and results are derived with a new simple approach. A functional model for the input RS symbol error probability is presented. Based on this new functional model, we compute the performance of a concatenated system in terms of RS word error probability, output RS symbol error probability, bit error probability due to decoding failure, and bit error probability due to decoding error. Finally we analyze the effects of the noisy carrier reference and the slow fading on the system performance.

Divsalar, D.

Cut-off rate calculations for the outer channel in a concatenated cooling system

Concatenated codes were long used as a practical means of achieving long block or constraint lengths for combating errors on very noisy channels. The inner and outer encoders are normally separated by an interleaver, so that decoded error bursts coming from the inner decoder are randomized before entering the outer decoder. The effectiveness of this interleaver is examined by calculating the cut-off rate of the outer channel seen by the outer decoder with and without interleaving. Interleaving never hurts the performance of a concatenated code, and when the inner code rate is near the cut-off rate of the inner channel, interleaving significantly improves code performance.

Herro, M. A.

Reliability and throughput analysis of a concatenated coding scheme

The performance of a concatenated coding scheme for error control in ARQ systems is analyzed for both random-noise and burst-noise channels. In particular, the probability of undetected error and the system throughput are calculated. In this scheme, the inner code is used for both error correction and error detection, and the outer code is used for error detection only. Interleaving/deinterleaving is assumed within the outer code. A retransmission is requested if either the inner code or the outer code detects the presence of errors. Various coding examples are considered. The results show that concatenated coding can provide extremely high system reliability (i.e., low probability of undetected error) and high system throughput.

Deng, Robert H.

A concatenated coded modulation scheme for error control

A concatenated coded modulation scheme for error control in data communications is presented. The scheme is achieved by concatenating a Reed-Solomon outer code and a bandwidth efficient block inner code for M-ary PSK modulation. Error performance of the scheme is analyzed for an AWGN channel. It is shown that extremely high reliability can be attained by using a simple M-ary PSK modulation inner code and relatively powerful Reed-Solomon outer code. Furthermore, if an inner code of high effective rate is used, the bandwidth expansion required by the scheme due to coding will be greatly reduced. The proposed scheme is particularly effective for high speed satellite communication for large file transfer where high reliability is required. Also presented is a simple method for constructing block codes for M-ary PSK modulation. Some short M-ary PSK codes with good minimum squared Euclidean distance are constructed. These codes have trellis structure and hence can be decoded with a soft decision Viterbi decoding algorithm.

Kasami, Tadao

A concatenated coded modulation scheme for error control

A concatenated coded modulation scheme for error control in data communications is presented. The scheme is achieved by concatenating a Reed-Solomon outer code and a bandwidth efficient block inner code for M-ary PSK modulation. Error performance of the scheme is analyzed for an AWGN channel. It is shown that extremely high reliability can be attained by using a simple M-ary PSK modulation inner code and a relatively powerful Reed-Solomon outer code. Furthermore, if an inner code of high effective rate is used, the bandwidth expansion required by the scheme due to coding will be greatly reduced. The proposed scheme is very effective for high speed satellite communications for large file transfer where high reliability is required. A simple method is also presented for constructing codes for M-ary PSK modulation. Some short M-ary PSK codes with good minimum squared Euclidean distance are constructed. These codes have trellis structure and hence can be decoded with a soft decision Viterbi decoding algorithm. Furthermore, some of these codes are phase invariant under multiples of 45 deg rotation.

Lin, Shu

A concatenated coded modulation scheme for error control (addition 2)

A concatenated coded modulation scheme for error control in data communications is described. The scheme is achieved by concatenating a Reed-Solomon outer code and a bandwidth efficient block inner code for M-ary PSK modulation. Error performance of the scheme is analyzed for an AWGN channel. It is shown that extremely high reliability can be attained by using a simple M-ary PSK modulation inner code and a relatively powerful Reed-Solomon outer code. Furthermore, if an inner code of high effective rate is used, the bandwidth expansion required by the scheme due to coding will be greatly reduced. The proposed scheme is particularly effective for high-speed satellite communications for large file transfer where high reliability is required. This paper also presents a simple method for constructing block codes for M-ary PSK modulation. Some short M-ary PSK codes with good minimum squared Euclidean distance are constructed. These codes have trellis structure and hence can be decoded with a soft-decision Viterbi decoding algorithm. Furthermore, some of these codes are phase invariant under multiples of 45 deg rotation.

Lin, Shu

High rate concatenated coding systems using bandwidth efficient trellis inner codes

High-rate concatenated coding systems with bandwidth-efficient trellis inner codes and Reed-Solomon (RS) outer codes are investigated for application in high-speed satellite communication systems. Two concatenated coding schemes are proposed. In one the inner code is decoded with soft-decision Viterbi decoding, and the outer RS code performs error-correction-only decoding (decoding without side information). In the other, the inner code is decoded with a modified Viterbi algorithm, which produces reliability information along with the decoded output. In this algorithm, path metrics are used to estimate the entire information sequence, whereas branch metrics are used to provide reliability information on the decoded sequence. This information is used to erase unreliable bits in the decoded output. An errors-and-erasures RS decoder is then used for the outer code. The two schemes have been proposed for high-speed data communication on NASA satellite channels. The rates considered are at least double those used in current NASA systems, and the results indicate that high system reliability can still be achieved.

Deng, Robert H.

A concatenated coded modulation scheme for error control

A concatenated coded modulation scheme for error control in data communications is presented. The scheme is achieved by concatenating a Reed-Solomon outer code and a bandwidth efficient block inner code for M-ary PSK modulation. Error performance of the scheme is analyzed for an AWGN channel. It is shown that extremely high reliability can be attained by using a simple M-ary PSK modulation inner code and relatively powerful Reed-Solomon outer code. Furthermore, if an inner code of high effective rate is used, the bandwidth expansion required by the scheme due to coding will be greatly reduced. The proposed scheme is particularly effective for high speed satellite communications for large file transfer where high reliability is required. Also presented is a simple method for constructing block codes for M-ary PSK modulation. Some short M-ary PSK codes with good minimum squared Euclidean distance are constructed. These codes have trellis structure and hence can be decoded with a soft-decision Viterbi decoding algorithm.

Kasami, Tadao

Performance of DBS-Radio using concatenated coding and equalization

The Direct Broadcast Satellite-Radio (DBS-R) receiver is being developed for operation in a multipath Rayleigh channel. This receiver uses equalization and concatenated coding, in addition to open loop and closed loop architectures for carrier demodulation and symbol synchronization. Performance test results of this receiver are presented in both AWGN and multipath Rayleigh channels. Simulation results show that the performance of the receiver operating in a multipath Rayleigh channel is significantly improved by using equalization. These results show that fractional-symbol equalization offers a performance advantage over full symbol equalization. Also presented is the base-line performance of the DBS-R receiver using concatenated coding and interleaving.

Gevargiz, J.

An Interactive Concatenated Turbo Coding System

This paper presents a concatenated turbo coding system in which a Reed-Solomon outer code is concatenated with a binary turbo inner code. In the proposed system, the outer code decoder and the inner turbo code decoder interact to achieve both good bit error and frame error performances. The outer code decoder helps the inner turbo code decoder to terminate its decoding iteration while the inner turbo code decoder provides soft-output information to the outer code decoder to carry out a reliability-based soft- decision decoding. In the case that the outer code decoding fails, the outer code decoder instructs the inner code decoder to continue its decoding iterations until the outer code decoding is successful or a preset maximum number of decoding iterations is reached. This interaction between outer and inner code decoders reduces decoding delay. Also presented in the paper are an effective criterion for stopping the iteration process of the inner code decoder and a new reliability-based decoding algorithm for nonbinary codes.

Liu, Ye

Performance Bounds on Two Concatenated, Interleaved Codes

A method has been developed of computing bounds on the performance of a code comprised of two linear binary codes generated by two encoders serially concatenated through an interleaver. Originally intended for use in evaluating the performances of some codes proposed for deep-space communication links, the method can also be used in evaluating the performances of short-block-length codes in other applications. The method applies, more specifically, to a communication system in which following processes take place: At the transmitter, the original binary information that one seeks to transmit is first processed by an encoder into an outer code (Co) characterized by, among other things, a pair of numbers (n,k), where n (n > k)is the total number of code bits associated with k information bits and n k bits are used for correcting or at least detecting errors. Next, the outer code is processed through either a block or a convolutional interleaver. In the block interleaver, the words of the outer code are processed in blocks of I words. In the convolutional interleaver, the interleaving operation is performed bit-wise in N rows with delays that are multiples of B bits. The output of the interleaver is processed through a second encoder to obtain an inner code (Ci) characterized by (ni,ki). The output of the inner code is transmitted over an additive-white-Gaussian- noise channel characterized by a symbol signal-to-noise ratio (SNR) Es/No and a bit SNR Eb/No. At the receiver, an inner decoder generates estimates of bits. Depending on whether a block or a convolutional interleaver is used at the transmitter, the sequence of estimated bits is processed through a block or a convolutional de-interleaver, respectively, to obtain estimates of code words. Then the estimates of the code words are processed through an outer decoder, which generates estimates of the original information along with flags indicating which estimates are presumed to be correct and which are found to be erroneous. From the perspective of the present method, the topic of major interest is the performance of the communication system as quantified in the word-error rate and the undetected-error rate as functions of the SNRs and the total latency of the interleaver and inner code. The method is embodied in equations that describe bounds on these functions. Throughout the derivation of the equations that embody the method, it is assumed that the decoder for the outer code corrects any error pattern of t or fewer errors, detects any error pattern of s or fewer errors, may detect some error patterns of more than s errors, and does not correct any patterns of more than t errors. Because a mathematically complete description of the equations that embody the method and of the derivation of the equations would greatly exceed the space available for this article, it must suffice to summarize by reporting that the derivation includes consideration of several complex issues, including relationships between latency and memory requirements for block and convolutional codes, burst error statistics, enumeration of error-event intersections, and effects of different interleaving depths. In a demonstration, the method was used to calculate bounds on the performances of several communication systems, each based on serial concatenation of a (63,56) expurgated Hamming code with a convolutional inner code through a convolutional interleaver. The bounds calculated by use of the method were compared with results of numerical simulations of performances of the systems to show the regions where the bounds are tight (see figure).

Moision, Bruce